[3dem] Fw: New cryoEM papers (#cryoem_papers)
Cheng Xingyi
xingyi.cheng at curie.fr
Thu Jan 9 04:07:01 PST 2025
Hey Alex,
Thank you for your ongoing efforts in sharing publication updates for our community!
I’m curious about how you manage your search.
If you or others are interested in automatically receiving updates on the latest papers related to cryo-EM and ET (or any other scientific topic), I’ve open-sourced my tool called Scitify.
It automates the retrieval of publications from arXiv, bioRxiv, and/or PubMed using your customised queries. Once set up, Scitify runs on its own, notifying you of updates daily, weekly, or as frequent as you'd like via email and/or Twitter.
Here are the links to Scitify and my Twitter bot (supported by Scitify) for updates on phase transition phenomena in bio-matter:
Scitify: https://urldefense.com/v3/__https://github.com/cyanching/Scitify__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFzWf9roQ$
Pha_Trans_Papers: https://urldefense.com/v3/__https://twitter.com/pha_tran_papers?lang=en__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFxEEdjgA$
Cheers,
Cyan
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Alex Noble <anoble at nysbc.org>
Sent: Wednesday, January 8, 2025 10:18 PM
To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] New cryoEM papers (#cryoem_papers)
Happy New Year cool people,
Alright, let's continue:
*
Elemental mapping in single-particle reconstructions by reconstructed electron energy-loss analysis
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02482-5__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG1Zz5uaQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02482-5__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaASNggz2w$>
*
Cryo-electron tomography in biology and medicine
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0940960209000697__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEtocQUAA$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0940960209000697__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDbvu904A$>
*
CryoVesNet: A Dedicated Framework for Synaptic Vesicle Segmentation in Cryo Electron Tomograms
https://urldefense.com/v3/__https://rupress.org/jcb/article-abstract/224/1/e202402169/277040/CryoVesNet-A-dedicated-framework-for-synaptic__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHxnYAl4Q$ <https://urldefense.com/v3/__https://rupress.org/jcb/article-abstract/224/1/e202402169/277040/CryoVesNet-A-dedicated-framework-for-synaptic__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAT5JPfzg$>
*
CryoSTAR: Leveraging Structural Prior and Constraints for Cryo-EM Heterogeneous Reconstruction
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02486-1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFoLqTodQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02486-1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBQUtFfsw$>
*
Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-53721-4__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFQOKzb9Q$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-53721-4__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBnIVj0nA$>
*
Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1047847724000881__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUExS5iTvw$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1047847724000881__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCz-iBDZQ$>
*
Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-52914-1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFeN4JtWg$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-52914-1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaALs7F3Mw$>
*
cryoMDM; Molecular simulation Driven structural Matching Approach to Estimate Variety of Atomic Three-dimensional Model Based on Noisy cryoEM Single Particle Images
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.31.621264v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFY5nCdEA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.31.621264v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCXr8JjJQ$>
*
REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers
https://urldefense.com/v3/__https://www.nature.com/articles/s42003-024-07045-0__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFHsTM0_g$ <https://urldefense.com/v3/__https://www.nature.com/articles/s42003-024-07045-0__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDQrSJ5yA$>
*
EMhub: a web platform for data management and on-the-fly processing in scientific facilities
https://urldefense.com/v3/__https://journals.iucr.org/d/issues/2024/11/00/vo5018/__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFXhNSgKg$ <https://urldefense.com/v3/__https://journals.iucr.org/d/issues/2024/11/00/vo5018/__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAfHl_XRg$>
*
Open-source Tools for CryoET Particle Picking Machine Learning Competitions
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.04.621608v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG4xU-VOA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.04.621608v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDAQZC5kw$>
*
Multi-species cryoEM calibration and workflow verification standard
https://urldefense.com/v3/__https://journals.iucr.org/f/issues/2024/11/00/rf5044/index.html__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGVhdfgkA$ <https://urldefense.com/v3/__https://journals.iucr.org/f/issues/2024/11/00/rf5044/index.html__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCbOOmc1A$>
*
Annotating CryoET Volumes: A Machine Learning Challenge
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.04.621686v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG03Xrldw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.04.621686v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDRNTkzBA$>
*
A comprehensive foundation model for cryo-EM image processing
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.04.621604v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEsvvqYwg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.04.621604v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBfKgqpLA$>
*
TomoPicker: Annotation-Efficient Particle Picking in cryo-electron Tomograms
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.04.620735v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGVTh2Iuw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.04.620735v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBw5or-Eg$>
*
Endosome rupture enables enteroviruses from the family Picornaviridae to infect cells
https://urldefense.com/v3/__https://www.nature.com/articles/s42003-024-07147-9__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF7_pjuTw$ <https://urldefense.com/v3/__https://www.nature.com/articles/s42003-024-07147-9__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC2GflJ7w$>
*
TomoScore: A Neural Network Approach for Quality Assessment of Cellular cryo-ET
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.06.622356v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEfpX57-w$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.06.622356v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAsEfnyMQ$>
*
Practical Considerations for Plunge Freezing Samples Over 40 °C for Cryo-EM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0968432824001628__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEdAJMtLw$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0968432824001628__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBiWh4law$>
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Hashing for Protein Structure Similarity Search
https://urldefense.com/v3/__https://arxiv.org/abs/2411.08286__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEjk7Xt0Q$ <https://urldefense.com/v3/__https://arxiv.org/abs/2411.08286__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAOiRikbw$>
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Ice thickness control and measurement in the VitroJet for time-efficient single particle structure determination
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S1047847724000790__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFlKiOHiQ$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S1047847724000790__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCoK1Pzhg$>
*
Proteomics Impact on Cell Biology to Resolve Cell Structure and Function
https://urldefense.com/v3/__https://www.mcponline.org/article/S1535-9476(24)00048-3/fulltext__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEIAOH-Kg$ <https://urldefense.com/v3/__https://www.mcponline.org/article/S1535-9476(24)00048-3/fulltext__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB8XKgouA$>
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Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S104784772400090X__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG3lLmspg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S104784772400090X__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCn1LDFPg$>
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RNA sample optimization for cryo-EM analysis
https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01072-1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG64oQmtg$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01072-1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCFbo7mBQ$>
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(Nature call for papers) Electron microscopy methods for nanoscale characterisation
https://urldefense.com/v3/__https://www.nature.com/collections/iafibeffjj__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE-L63zdw$ <https://urldefense.com/v3/__https://www.nature.com/collections/iafibeffjj__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBtBqAlcw$>
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Improved automated model building for cryo-EM maps using CryFold
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.13.623164v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF393Ewrw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.13.623164v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCU3gdlow$>
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Sequence modeling and design from molecular to genome scale with Evo
https://urldefense.com/v3/__https://www.science.org/doi/10.1126/science.ado9336__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEgF5A_mw$ <https://urldefense.com/v3/__https://www.science.org/doi/10.1126/science.ado9336__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAqCvI_5w$>
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Semantic segmentation-based detection algorithm for challenging cryo-electron microscopy RNP samples
https://urldefense.com/v3/__https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2024.1473609/full__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHaMFeQ6g$ <https://urldefense.com/v3/__https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2024.1473609/full__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBm4rhmpw$>
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Overcoming the preferred-orientation problem in cryo-EM with self-supervised deep learning
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02505-1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEf1DtVig$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02505-1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA6-XGkkA$>
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Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.20.623795v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFRhQZeqA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.20.623795v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCbnbSzfw$>
*
Estimating the tails of the spectrum of the Hessian of the log-likelihood for ab-initio single-particle reconstruction in electron cryomicroscopy
https://urldefense.com/v3/__https://arxiv.org/abs/2411.13263__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE-o_sLLg$ <https://urldefense.com/v3/__https://arxiv.org/abs/2411.13263__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD12u6tKg$>
*
De novo identification of protein domains in cryo-electron tomography maps from AlphaFold2 models
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.21.623534v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFj52ZpGQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.21.623534v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBrupCqJQ$>
*
Laser Flash Melting Cryo-EM Samples to Overcome Preferred Orientation
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.21.624652v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGwwGeIIw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.21.624652v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC2mbpHJA$>
*
Practical Guide for Implementing Cryogenic Electron Microscopy Structure Determination in Dermatology Research
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0022202X24028768__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF5-cGDSw$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0022202X24028768__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCViWBmaw$>
*
Chai-1: Decoding the molecular interactions of life
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.10.615955v2__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEULaCkig$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.10.615955v2__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBj9keYOA$>
*
Boltz-1 Democratizing Biomolecular Interaction Modeling
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.19.624167v2__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHjVp0Ovg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.19.624167v2__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAD5SnB8A$>
*
TOMOMAN: a software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/iucr/doi/10.1107/S1600576724010264__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFyAJz7rw$ <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/iucr/doi/10.1107/S1600576724010264__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCFDL7wGw$>
*
Passage through micro-sprayer increases functional activity-implications for activity assays in time-resolved cryo-EM
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.01.624867v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFYRhVG0A$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.01.624867v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDjWHIzVw$>
*
Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.01.626131v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFX9VR3uA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.01.626131v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAIeFDq0w$>
https://urldefense.com/v3/__https://git.biohpc.swmed.edu/rosen-lab/catm__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG7yebYig$ <https://urldefense.com/v3/__https://git.biohpc.swmed.edu/rosen-lab/catm__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDR9QOpjw$>
*
Improving AlphaFold 3 structural modeling by incorporating explicit crosslinks
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.03.626671v2__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFC4LP8rg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.03.626671v2__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDKMeN1zQ$>
*
AlphaPulldown2 - A General Pipeline for High-Throughput Structural Modeling
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.28.625873v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEHzLdMsg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.11.28.625873v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCW_9kN2A$>
*
Open architecture of archaea MCM and dsDNA complexes resolved using monodispersed streptavidin affinity CryoEM
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-53745-w__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHJuX2KGQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-53745-w__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAfI504Fg$>
*
Orientation Determination of Cryo-EM Images Using Block Stochastic Riemannian Subgradient Methods
https://urldefense.com/v3/__https://arxiv.org/abs/2411.14021__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGQhcO1eQ$ <https://urldefense.com/v3/__https://arxiv.org/abs/2411.14021__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDyYfcxZw$>
*
Flexible fitting of AlphaFold2-Predicted models to Cryo-EM density maps using elastic network models: a methodical affirmation
https://urldefense.com/v3/__https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae181/7903278__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEJjQERvQ$ <https://urldefense.com/v3/__https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae181/7903278__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDcp4eW7Q$>
*
The combined focal loss and dice loss function improves the segmentation of beta-sheets in medium-resolution cryo-electron-microscopy density maps
https://urldefense.com/v3/__https://academic.oup.com/bioinformaticsadvances/article/4/1/vbae169/7907198__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUH2WGxhLA$ <https://urldefense.com/v3/__https://academic.oup.com/bioinformaticsadvances/article/4/1/vbae169/7907198__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDDkCYjOA$>
*
J-Invariant Volume Shuffle for Self-Supervised Cryo-Electron Tomogram Denoising on Single Noisy Volume
https://urldefense.com/v3/__https://www.arxiv.org/abs/2411.15248__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEjYsrP4A$ <https://urldefense.com/v3/__https://www.arxiv.org/abs/2411.15248__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDQmDz9tw$>
*
Bayesian Perspective for Orientation Estimation in Cryo-EM and Cryo-ET
https://urldefense.com/v3/__https://arxiv.org/abs/2412.03723v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFyRNj9Bw$ <https://urldefense.com/v3/__https://arxiv.org/abs/2412.03723v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDDuk-Lsw$>
*
SynapseNet: Deep Learning for Automatic Synapse Reconstruction
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.02.626387v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFPq_GMlg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.02.626387v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDt1fyTbA$>
https://urldefense.com/v3/__https://github.com/computational-cell-analytics/synapse-net__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHS8TwJMA$ <https://urldefense.com/v3/__https://github.com/computational-cell-analytics/synapse-net__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCIfTHexQ$>
*
Time-resolved cryo-EM (TRCEM) sample preparation using a PDMS-based microfluidic chip assembly
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.08.627437v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHY9rOLpg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.08.627437v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDigPhRlA$>
*
In situ structural analysis of mammalian cells using a 200 kV electron cryomicroscope: implications for research infrastructure
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.06.627167v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE-YelqdA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.06.627167v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBcODcXzA$>
*
The big chill: Growth of in situ structural biology with cryo-electron tomography
https://urldefense.com/v3/__https://www.cambridge.org/core/journals/qrb-discovery/article/big-chill-growth-of-in-situ-structural-biology-with-cryoelectron-tomography/36A704E4FFFB5AB2D6AEC3F7156BA90A__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE6pjb13A$ <https://urldefense.com/v3/__https://www.cambridge.org/core/journals/qrb-discovery/article/big-chill-growth-of-in-situ-structural-biology-with-cryoelectron-tomography/36A704E4FFFB5AB2D6AEC3F7156BA90A__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCu68EPEA$>
*
Cryo-EM images are intrinsically low dimensional
https://urldefense.com/v3/__https://www.mlsb.io/papers_2024/Cryo-EM_images_are_intrinsically_low_dimensional.pdf__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHeEPy5Ng$ <https://urldefense.com/v3/__https://www.mlsb.io/papers_2024/Cryo-EM_images_are_intrinsically_low_dimensional.pdf__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAP1CE90w$>
*
ProPicker: Promptable Segmentation for Particle Picking in Cryogenic Electron Tomography
https://urldefense.com/v3/__https://www.mlsb.io/papers_2024/ProPicker:_Promptable_Segmentation_for_Particle_Picking_in_Cryogenic_Electron_Tomography.pdf__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGIJazdwg$ <https://urldefense.com/v3/__https://www.mlsb.io/papers_2024/ProPicker:_Promptable_Segmentation_for_Particle_Picking_in_Cryogenic_Electron_Tomography.pdf__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCoQaNJQg$>
*
Mixture of neural fields for heterogeneous reconstruction in cryo-EM
https://urldefense.com/v3/__https://arxiv.org/abs/2412.09420__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFf1u1U7Q$ <https://urldefense.com/v3/__https://arxiv.org/abs/2412.09420__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD50QogcQ$>
*
Recognizing amino acid sidechains in a medium resolution cryo-electron density map
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.10.627859v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFpFjPcwg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.10.627859v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAxAf3oZQ$>
*
Depositing biological segmentation datasets FAIRly
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.10.627814v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFIjGihSQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.10.627814v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBYrBhvEg$>
*
Enhancing the Electron Radiation Resistance of Macromolecules in Cryo-TEM Imaging Using Sodium Ascorbate
https://urldefense.com/v3/__https://pubs.acs.org/doi/10.1021/acs.macromol.4c02108__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUH1a4bE9w$ <https://urldefense.com/v3/__https://pubs.acs.org/doi/10.1021/acs.macromol.4c02108__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDA-544wg$>
*
Modeling Bias Toward Binding Sites in PDB Structural Models
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.14.628518v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUENOGTUag$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.14.628518v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBZ0__-4A$>
*
Cryo-EM reconstruction of helical polymers: Beyond the simple cases
https://urldefense.com/v3/__https://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/cryoem-reconstruction-of-helical-polymers-beyond-the-simple-cases/F9ED5390A396E502657F02D7D27773C6__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHaj0Fj8w$ <https://urldefense.com/v3/__https://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/cryoem-reconstruction-of-helical-polymers-beyond-the-simple-cases/F9ED5390A396E502657F02D7D27773C6__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBHuIDvZQ$>
*
UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs
https://urldefense.com/v3/__https://academic.oup.com/bib/article/26/1/bbae636/7919967__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF8kYlfqA$ <https://urldefense.com/v3/__https://academic.oup.com/bib/article/26/1/bbae636/7919967__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC9C8qkew$>
*
Cryo-electron tomography: en route to the molecular anatomy of organisms and tissues
https://urldefense.com/v3/__https://portlandpress.com/biochemsoctrans/article/doi/10.1042/BST20240173/235350/Cryo-electron-tomography-en-route-to-the-molecular__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHVLPzcKw$ <https://urldefense.com/v3/__https://portlandpress.com/biochemsoctrans/article/doi/10.1042/BST20240173/235350/Cryo-electron-tomography-en-route-to-the-molecular__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD7GykcNQ$>
*
Automatic detection of alignment errors in cryo-electron tomography
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S1047847724000935__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHS6AcmmQ$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S1047847724000935__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCkqT3DIg$>
*
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM
https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01088-7__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFlrYag4w$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01088-7__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD8qvgV4w$>
*
Preparing submicrometer crystals for electron diffraction
https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01098-5__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFViq6cKQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01098-5__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDUjFHhUw$>
*
Diffusion priors for Bayesian 3D reconstruction from incomplete measurements
https://urldefense.com/v3/__https://arxiv.org/abs/2412.14897v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFLpkSFcQ$ <https://urldefense.com/v3/__https://arxiv.org/abs/2412.14897v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBWSVObxw$>
*
Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.19.629196v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHThV5EeQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.19.629196v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCXT7TWDQ$>
*
Radiation damage behavior of soft matter in ultrafast cryo-electron microscopy (cryo-UEM)
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.20.629524v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF4KKfcug$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.20.629524v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA8mNHgfA$>
*
cryoTIGER: Deep-Learning Based Tilt Interpolation Generator for Enhanced Reconstruction in Cryo Electron Tomography
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.17.628939v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFrqe2NYg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.17.628939v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDUQ74Rng$>
*
CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples
https://urldefense.com/v3/__https://elifesciences.org/articles/97227__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGiZxrkCw$ <https://urldefense.com/v3/__https://elifesciences.org/articles/97227__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCIJ2cCiQ$>
*
Demonstrating Soft X-Ray Tomography in the lab for correlative cryogenic biological imaging using X-rays and light microscopy
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.23.629889v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHI4oPMyQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.23.629889v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBuzb2p8A$>
*
Orientation Determination of Cryo-EM Projection Images Using Reliable Common Lines and Spherical Embeddings
https://urldefense.com/v3/__https://ieeexplore.ieee.org/document/10711260__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEGShWIwQ$ <https://urldefense.com/v3/__https://ieeexplore.ieee.org/document/10711260__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCb6aEgng$>
*
Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.28.630444v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE5dwUxTQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.12.28.630444v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA6Eq9Gvg$>
*
A fiducial-assisted strategy compatible with resolving small MFS transporter structures in multiple conformations using cryoEM
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-54986-5__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHoPBz7UQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-54986-5__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBriG-a1Q$>
*
High-resolution cryo-EM using a common LaB6 120-keV electron microscope equipped with a sub–200-keV direct electron detector
https://urldefense.com/v3/__https://www.science.org/doi/10.1126/sciadv.adr0438__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG5YwyhCA$ <https://urldefense.com/v3/__https://www.science.org/doi/10.1126/sciadv.adr0438__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDgTzbBtw$>
*
MPicker: visualizing and picking membrane proteins for cryo-electron tomography
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-55767-w__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFZDJnloA$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-55767-w__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCmrFb5ew$>
I'll be posting from my gmail account (alexjnoble at gmail.com) starting next time.
Best wishes,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Tuesday, October 22, 2024 5:00 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi all,
I was sick yesterday, so today is paper day!
*
DRACO: A Denoising-Reconstruction Autoencoder for Cryo-EM
https://urldefense.com/v3/__https://arxiv.org/abs/2410.11373v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEFeEZeWA$ <https://urldefense.com/v3/__https://arxiv.org/abs/2410.11373v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBEBYeZLQ$>
*
Crossed laser phase plates for transmission electron microscopy
https://urldefense.com/v3/__https://arxiv.org/abs/2410.11328v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUH3rVMiTw$ <https://urldefense.com/v3/__https://arxiv.org/abs/2410.11328v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAxqBooKg$>
*
A data portal for providing standardized annotations for cryo-electron tomography
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02477-2__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGWmiqMbg$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02477-2__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD5D7HtAw$>
*
DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02479-0__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHBJVdC7A$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02479-0__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC_93UjJg$>
*
Simulation-based inference of single-molecule experiments
https://urldefense.com/v3/__https://arxiv.org/abs/2410.15896__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF-ZTTXWw$ <https://urldefense.com/v3/__https://arxiv.org/abs/2410.15896__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAe_SjMmA$>
*
CryoLike: A python package for cryo-electron microscopy image-to-structure likelihood calculations
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.18.619077v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUH55ja4hw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.18.619077v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBYB9Sf6g$>
Best regards,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Tuesday, October 15, 2024 10:04 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi all,
I took a week off. CryoEM-relater papers from the last 2 weeks:
*
New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.01.616095v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGy5u3tTw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.01.616095v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCdtLOrzg$>
*
Recent advances in correlative cryo-light and electron microscopy
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X24001611__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF-46KlZg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X24001611__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaATpyt8_A$>
*
Representing structures of the multiple conformational states of proteins
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X2300177X__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGclkFlCQ$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X2300177X__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB6ql08vQ$>
*
CryoSPIN: Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference
https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEoy3Ov8A$ <https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBeEdl0Gg$>
*
Automated model-free analysis of cryo-EM volume ensembles with SIREn
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.08.617123v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFS4w1FKg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.08.617123v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAGFkiT2Q$>
*
Subspace method of moments for ab initio 3-D single-particle Cryo-EM reconstruction
https://urldefense.com/v3/__https://arxiv.org/abs/2410.06889__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGX6al9QA$ <https://urldefense.com/v3/__https://arxiv.org/abs/2410.06889__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCGTPYRFw$>
*
Image Detection Using Combinatorial Auction
https://urldefense.com/v3/__https://ieeexplore.ieee.org/document/10637697__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGf2QsqoQ$ <https://urldefense.com/v3/__https://ieeexplore.ieee.org/document/10637697__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC9Ggg6gA$>
*
Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-53116-5__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHwVeQF_w$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-53116-5__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDcEUCz_A$>
*
Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.07.617120v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGb85Nagw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.07.617120v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBFPjTYyw$>
*
An approach for coherent periodogram averaging of tilt-series data for improved CTF estimation
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.10.617684v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFSBkItEw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.10.617684v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDXPO6GFg$>
*
ExoSloNano: Multi-Modal Nanogold Tags for identi-fication of Macromolecules in Live Cells & Cryo-Electron Tomograms
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.12.617288v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGHsNjpDQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.10.12.617288v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDEeZ4Qng$>
*
Easy and accurate protein structure prediction using ColabFold
https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01060-5__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGhXAfTJw$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01060-5__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB-4b4pVg$>
*
GoToCloud optimization of cloud computing environment for accelerating cryo-EM structure-based drug design
https://urldefense.com/v3/__https://www.nature.com/articles/s42003-024-07031-6__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGZI-kWzw$ <https://urldefense.com/v3/__https://www.nature.com/articles/s42003-024-07031-6__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB7sg5PrA$>
*
Roodmus: a toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions
https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2024/06/00/rq5011/index.html__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEy66K9XA$ <https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2024/06/00/rq5011/index.html__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB5N2d23g$>
*
CryoFM: A Flow-based Foundation Model for Cryo-EM Densities
https://urldefense.com/v3/__https://arxiv.org/abs/2410.08631__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEeOMaiJA$ <https://urldefense.com/v3/__https://arxiv.org/abs/2410.08631__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBC7cLxPg$>
*
CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy
https://urldefense.com/v3/__https://www.pnas.org/doi/10.1073/pnas.2417046121__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHfVMYu0g$ <https://urldefense.com/v3/__https://www.pnas.org/doi/10.1073/pnas.2417046121__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDRkMVuuA$>
Best regards,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, September 30, 2024 11:36 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi all,
End-of-day paper posting, and a reminder that these emails can be filtered using the #cryoem_papers tag in the title.
*
A deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-51438-y__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHLjZ84_A$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-51438-y__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCYWs0Fkw$>
*
Camera Paths, Modeling, and Image Processing Tools for ArtiaX
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.23.614454v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGVbOl1cQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.23.614454v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAxOT3hHQ$>
*
OPUS-DSD2: Disentangling Dynamics and Compositional Heterogeneity for Cryo-EM Single Particle Analysis
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.24.614854v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFMmvwhjQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.24.614854v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA-phOVpg$>
*
Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.27.615511v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG2aVL4jg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.27.615511v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCTXdJXDA$>
*
VirtualIce: Half-synthetic CryoEM Micrograph Generator
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.28.615520v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEU9a6d7Q$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.28.615520v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCXKspOnw$>
Best wishes,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, September 23, 2024 5:11 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi cool people,
Below is a list of new cryoEM-related material from the past week. Sorry for the delay, I've been working on software and a paper which should be out soon!
*
Bridging structural biology and clinical research through in-tissue cryo-electron tomography
https://urldefense.com/v3/__https://www.embopress.org/doi/full/10.1038/s44318-024-00216-z__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE9z4wENA$ <https://urldefense.com/v3/__https://www.embopress.org/doi/full/10.1038/s44318-024-00216-z__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDsg4AoLA$>
*
Single particle cryo-EM map and model validation: It's not crystal clear
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24001453__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG9jb4JFg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24001453__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB6HGGVzw$>
*
The future of integrated structural biology
https://urldefense.com/v3/__https://www.cell.com/structure/fulltext/S0969-2126(24)00331-9__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEryAa8jw$ <https://urldefense.com/v3/__https://www.cell.com/structure/fulltext/S0969-2126(24)00331-9__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDC8xIBOg$>
*
pytom-match-pick: a tophat-transform constraint for automated classification in template matching
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.17.613497v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFBLvBj-w$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.17.613497v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAnh5x4Jg$>
*
Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.16.613176v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUH0Ds58gw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.16.613176v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAXXQ410A$>
*
Integrating various Experimental Information to Assist Protein Complex Structure Prediction by GRASP
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.16.613256v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEUNeoevA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.16.613256v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA3AXq83w$>
*
How to autocontouring grid squares in SerialEM:
https://urldefense.com/v3/__https://x.com/Nexperion/status/1836681264499139055__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEHzek9xA$ <https://urldefense.com/v3/__https://x.com/Nexperion/status/1836681264499139055__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAenXNvtw$>
Best wishes,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, September 16, 2024 10:54 AM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi cool people,
Below are cryoEM-related papers and software from the past week:
*
The Protein Design Archive (PDA): insights from 40 years of protein design
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.05.611465v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGJcZK5Zg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.05.611465v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBn-dq1qw$>
*
Fast event-based electron counting for small molecule structure determination by MicroED
https://urldefense.com/v3/__https://chemrxiv.org/engage/chemrxiv/article-details/66db946ecec5d6c1425cd490__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGfsBtKWQ$ <https://urldefense.com/v3/__https://chemrxiv.org/engage/chemrxiv/article-details/66db946ecec5d6c1425cd490__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAdcPglBA$>
*
Outlier Removal in Cryo-EM via Radial Profiles
https://urldefense.com/v3/__https://arxiv.org/abs/2409.05523__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEyffyvPw$ <https://urldefense.com/v3/__https://arxiv.org/abs/2409.05523__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBEMvxYQQ$>
*
Preparing research samples for safe arrival at centers and facilities: recipes for successful experiments
https://urldefense.com/v3/__https://journals.iucr.org/f/issues/2024/08/00/oq5002/index.html__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEEFHBygQ$ <https://urldefense.com/v3/__https://journals.iucr.org/f/issues/2024/08/00/oq5002/index.html__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBjaivJXw$>
*
Development of a Liquid-Helium Free Cryogenic Sample Holder with mK Temperature Control for Autonomous Electron Microscopy
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0304399124001165__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEY2NfMYA$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0304399124001165__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDgXIXdzA$>
*
Genetically Encoded FerriTag as a Specific Label for Cryo-Electron Tomography
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.10.612178v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGTJ8BRSw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.10.612178v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDX6ri2cw$>
*
Cryo-Electron Microscopy in Structural Biology (book)
https://urldefense.com/v3/__https://www.taylorfrancis.com/books/edit/10.1201/9781003326106/cryo-electron-microscopy-structural-biology-krishnarao-appasani__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGNEKv6dA$ <https://urldefense.com/v3/__https://www.taylorfrancis.com/books/edit/10.1201/9781003326106/cryo-electron-microscopy-structural-biology-krishnarao-appasani__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC2TpblIQ$>
*
Single-Particle Cryo-EM: What happens inside the Black Box?
https://urldefense.com/v3/__https://osf.io/preprints/osf/5empt__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHyOVbFCg$ <https://urldefense.com/v3/__https://osf.io/preprints/osf/5empt__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAaSIemdw$>
*
Precision defect integrated graphene as reliable support membrane for high-resolution cryo-transmission electron microscopy
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0008622324008443__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGav51EFw$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0008622324008443__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAU7klhBA$>
*
CryoTEN: Efficiently Enhancing Cryo-EM Density Maps Using Transformers
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.06.611715v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFsJpcVuw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.06.611715v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC-iyYOkA$>
*
Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics
https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/25/17/9725__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHpXCp_WQ$ <https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/25/17/9725__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDFjpREEw$>
*
Evaluating Cryo-TEM Reconstruction Accuracy of Self-Assembled Polymer Nanostructures
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/marc.202400589__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHYB28eSw$ <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/marc.202400589__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCY7KdCPQ$>
*
Serialized on-grid lift-in sectioning for tomography (SOLIST) enables a biopsy at the nanoscale
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02384-6__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHf8sDQKQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02384-6__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBG5tdxEA$>
*
Serial lift-out for in situ structural biology of multicellular specimens
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02317-3__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFwP9K2Cg$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02317-3__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBEh-QkwA$>
*
Protein identification using cryo-EM and artificial intelligence guides improved sample purification
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.11.612515v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGuAzEwDg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.11.612515v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCE0zhZoA$>
*
Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-52403-5__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHv5YHI7A$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-52403-5__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCIIgbyyA$>
*
Academic Journal Publishers Antitrust Litigation
https://urldefense.com/v3/__https://www.lieffcabraser.com/antitrust/academic-journals/__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHAsowpAg$ <https://urldefense.com/v3/__https://www.lieffcabraser.com/antitrust/academic-journals/__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDOYov3Yg$>
"... these publishers conspired to unlawfully appropriate billions of dollars that would otherwise have funded scientific research."
*
Uniprot to AlphaFold3 JSON Generator (Beta)
https://urldefense.com/v3/__https://uniprot2alphafold3.streamlit.app/__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFJ2cWCbw$ <https://urldefense.com/v3/__https://uniprot2alphafold3.streamlit.app/__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAoI4MLYA$>
https://urldefense.com/v3/__https://x.com/DawidZyla/status/1835077103630664087__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHNLKmwVQ$ <https://urldefense.com/v3/__https://x.com/DawidZyla/status/1835077103630664087?s=19__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDIrVu_MA$>
Best wishes,
Alex Noble
(written only on behalf of myself, not anyone else=)
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, September 9, 2024 11:02 AM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi cool people,
Here's last week set of new cryoEM-related papers and software:
*
Technical Report of HelixFold3 for Biomolecular Structure Prediction
https://urldefense.com/v3/__https://arxiv.org/abs/2408.16975__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHHKn81jg$ <https://urldefense.com/v3/__https://arxiv.org/abs/2408.16975__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAjnM8J9w$>
https://urldefense.com/v3/__https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEqClO0fg$ <https://urldefense.com/v3/__https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAFcCJ0JA$>
https://urldefense.com/v3/__https://paddlehelix.baidu.com/__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGUINGqDw$ <https://urldefense.com/v3/__https://paddlehelix.baidu.com/__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDbgmm2aA$>
*
Cryo-EM: A window into the dynamic world of RNA molecules
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400143X__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFueMll_w$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400143X__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaApJZrWFg$>
*
Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-52091-1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGLEpIIIA$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-52091-1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB4FDXNPQ$>
*
Mesoscale Explorer - Visual Exploration of Large-Scale Molecular Models
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.02.610826v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHQs-fguQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.02.610826v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCyAAAQDw$>
*
Teaching protein structure and function through molecular visualization
https://urldefense.com/v3/__https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.21860__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEtRahiOQ$ <https://urldefense.com/v3/__https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.21860__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD_vX2DFw$>
*
Tomogram Reconstruction and Gold Fiducial Removal with Warp, Etomo, and Fidder
https://urldefense.com/v3/__https://www.protocols.io/view/tomogram-reconstruction-and-gold-fiducial-removal-6qpvr8qbblmk/v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFNrEmdKQ$ <https://urldefense.com/v3/__https://www.protocols.io/view/tomogram-reconstruction-and-gold-fiducial-removal-6qpvr8qbblmk/v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBoSQbKfg$>
*
De novo design of high-affinity protein binders with AlphaProteo
https://urldefense.com/v3/__https://deepmind.google/discover/blog/alphaproteo-generates-novel-proteins-for-biology-and-health-research/__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFHzvqdmw$ <https://urldefense.com/v3/__https://deepmind.google/discover/blog/alphaproteo-generates-novel-proteins-for-biology-and-health-research/__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCPeyYyBw$>
https://urldefense.com/v3/__https://storage.googleapis.com/deepmind-media/DeepMind.com/Blog/alphaproteo-generates-novel-proteins-for-biology-and-health-research/AlphaProteo2024.pdf__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGloIVEjA$ <https://urldefense.com/v3/__https://storage.googleapis.com/deepmind-media/DeepMind.com/Blog/alphaproteo-generates-novel-proteins-for-biology-and-health-research/AlphaProteo2024.pdf__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCmXD59Dw$>
*
Deep Mapper: Efficient Visualization of Plausible Conformational Pathways
https://urldefense.com/v3/__https://arxiv.org/abs/2402.19177__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUH1VfdprQ$ <https://urldefense.com/v3/__https://arxiv.org/abs/2402.19177__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAGLaUT7w$>
*
Liquid Phase Electron Microscopy of Bacterial Ultrastructure
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202402871__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGN7KEAjg$ <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202402871__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBw4sQRQA$>
*
Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE
https://urldefense.com/v3/__https://elifesciences.org/articles/99702__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGQvCpJMg$ <https://urldefense.com/v3/__https://elifesciences.org/articles/99702__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA6ylTlCQ$>
*
Dynamic PDB: A New Dataset and a SE(3) Model Extension by Integrating Dynamic Behaviors and Physical Properties in Protein Structures
https://urldefense.com/v3/__https://arxiv.org/abs/2408.12413__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUH6MB6f3A$ <https://urldefense.com/v3/__https://arxiv.org/abs/2408.12413__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBxdBKFlA$>
*
Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.05.611417v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGqbX2v1Q$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.09.05.611417v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBj7-9ung$>
*
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02403-6__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEnh42w-g$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02403-6__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAOTgyxyg$>
*
Cryo-Electron Microscopy Studies of Biomolecular Structure and Dynamics
https://urldefense.com/v3/__https://www.mdpi.com/2072-666X/15/9/1092__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHwLinl2A$ <https://urldefense.com/v3/__https://www.mdpi.com/2072-666X/15/9/1092__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC4N9k2Ww$>
*
AlphaFold3 Open-Source Implementation
https://urldefense.com/v3/__https://github.com/Ligo-Biosciences/AlphaFold3__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGFt-yfjQ$ <https://urldefense.com/v3/__https://github.com/Ligo-Biosciences/AlphaFold3__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAfVxcbrw$>
https://urldefense.com/v3/__https://x.com/ArdaGoreci/status/1830744265007480934__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHQAellBA$ <https://urldefense.com/v3/__https://x.com/ArdaGoreci/status/1830744265007480934__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDgvtAXOw$>
Best wishes,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, September 2, 2024 8:23 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi cool people,
Below is the last week's set of new cryoEM papers and software:
*
Applying 3D ED/MicroED workflows toward the next frontiers
https://urldefense.com/v3/__https://journals.iucr.org/c/issues/2024/06/00/yp3235/index.html__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHFCQUMyg$ <https://urldefense.com/v3/__https://journals.iucr.org/c/issues/2024/06/00/yp3235/index.html__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDc0n0dhw$>
*
CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM
https://urldefense.com/v3/__https://www.nature.com/articles/s42003-024-06739-9__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHPmoNWlQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s42003-024-06739-9__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCRBa8tVA$>
*
A Cryo-to-Liquid Phase Correlative Light Electron Microscopy Workflow for the Visualization of Biological Processes in Graphene Liquid Cells
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2023.05.08.539575v2__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE-G2Bm1Q$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2023.05.08.539575v2__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBl2MTMSg$>
*
Artificial Intelligence in Cryo-EM Protein Particle Picking: The Hope, Hype, and Hurdles
https://urldefense.com/v3/__https://www.preprints.org/manuscript/202408.1936/v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGUMNbHuQ$ <https://urldefense.com/v3/__https://www.preprints.org/manuscript/202408.1936/v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCNM4Q1JQ$>
*
Ligand Identification using Deep Learning
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.27.610022v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEFfeWmdQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.27.610022v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBN0ZzB7Q$>
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Energy filtering enables macromolecular MicroED data at sub-atomic resolution
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.29.610380v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGOBnKGyg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.29.610380v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaByFOC_EA$>
*
Validation of 3D cryoEM single particle reconstruction correctness and handedness with Ewald's sphere correction
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.29.610390v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHTYiWfZQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.29.610390v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDNFL9EPQ$>
*
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding
https://urldefense.com/v3/__https://arxiv.org/abs/2408.11363__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHz6yvGtA$ <https://urldefense.com/v3/__https://arxiv.org/abs/2408.11363__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAfggpErg$>
*
Targeting TRP channels: The emerging role of cryogenic electron microscopy in drug discovery (book chapter)
https://urldefense.com/v3/__https://wzww.sciencedirect.com/science/article/abs/pii/B9780443186530000101__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGPYZY9ug$ <https://urldefense.com/v3/__https://wzww.sciencedirect.com/science/article/abs/pii/B9780443186530000101__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDkLc7mEA$>
*
Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser
https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2024/05/00/fq5024/index.html__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUH-sa-gkw$ <https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2024/05/00/fq5024/index.html__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDzIeF08g$>
*
Wiggle for UCSF ChimeraX
https://urldefense.com/v3/__https://x.com/bj_charles/status/1567346827456028673__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHJpg-Zmw$ <https://urldefense.com/v3/__https://x.com/bj_charles/status/1567346827456028673__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC4FO_2Tg$>
https://urldefense.com/v3/__https://github.com/charbj/wiggle__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHUu_C5nQ$ <https://urldefense.com/v3/__https://github.com/charbj/wiggle__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAfllZPzg$>
*
maskChains for ChimeraX
https://urldefense.com/v3/__https://x.com/JiangLabCryoEM/status/1828861099485073537__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGFm1rhmw$ <https://urldefense.com/v3/__https://x.com/JiangLabCryoEM/status/1828861099485073537__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCL1urx4w$>
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Technical Report of HelixFold3 for Biomolecular Structure Prediction
https://urldefense.com/v3/__https://arxiv.org/abs/2408.16975__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHHKn81jg$ <https://urldefense.com/v3/__https://arxiv.org/abs/2408.16975__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAjnM8J9w$>
https://urldefense.com/v3/__https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEqClO0fg$ <https://urldefense.com/v3/__https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAFcCJ0JA$>
https://urldefense.com/v3/__https://paddlehelix.baidu.com/?redirect__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFfVDJbXQ$ <https://urldefense.com/v3/__https://paddlehelix.baidu.com/?redirect__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCsxkHwwg$>
Cheers,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, August 26, 2024 1:17 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi cool people,
Below is this past week's installment of new cryoEM papers (including several that are on the edge of the field):
*
MAASTY: A (dis)ordered copolymer for structural determination of human membrane proteins in native nanodiscs
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.19.608676v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEMjoiKpA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.19.608676v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB5g-K9oA$>
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Generative artificial intelligence performs rudimentary structural biology modeling
https://urldefense.com/v3/__https://www.nature.com/articles/s41598-024-69021-2__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE_1Xcx-Q$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41598-024-69021-2__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD-DAGTZQ$>
*
Miniaturizing, Modifying, and Augmenting Nature’s Proteins with Raygun
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.13.607858v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHawCt2Ew$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.13.607858v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDReOYU3Q$>
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Lifting the Concentration Limit of Mass Photometry by PEG Nanopatterning
https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acs.nanolett.4c01667__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFzR_7X4w$ <https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acs.nanolett.4c01667__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDJIZFueA$>
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CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM
https://urldefense.com/v3/__https://arxiv.org/abs/2408.05526__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUETleAWNQ$ <https://urldefense.com/v3/__https://arxiv.org/abs/2408.05526__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBTR8nJVQ$>
*
Methods in Cell Biology chapters:
*
How to apply the broad toolbox of correlative light and electron microscopy to address a specific biological question
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X2400061X__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFpaBcNxg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X2400061X__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB89lLmjA$>
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Correlative cryo-microscopy pipelines for in situ cellular studies
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000694__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFcysvI8Q$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000694__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBij-pQyg$>
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Building a super-resolution fluorescence cryomicroscope
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000578__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGjK3Pcnw$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000578__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCEXLk_GQ$>
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Imaging intracellular components in situ using super-resolution cryo-correlative light and electron microscopy
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X2400058X__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEsX96hsw$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X2400058X__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBkYERGqw$>
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Toward quantitative super-resolution methods for cryo-CLEM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000591__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE5tw03yQ$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000591__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDF7oLsLw$>
*
Recent Technical Advances in Cellular Cryo-Electron Tomography
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1357272524001407__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGZIaJ-RQ$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1357272524001407__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBWyb7WXg$>
*
Advancing Single-Particle Analysis in Synthetic Chemical Systems: A Forward-Looking Discussion
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/adma.202406914__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEn04BQag$ <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/adma.202406914__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD8givmYg$>
*
Imaging Frozen, Hydrated Acrosomal Bundle from Limulus Sperm at 7 Å Resolution with a 400 kV Electron Cryomicroscope
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0022283683711551__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFyyhqJ0Q$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0022283683711551__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC1Lmpjug$>
*
Self-assembled superstructure alleviates air-water interface effect in cryo-EM
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-51696-w__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEL-o6z_Q$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-51696-w__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDMM7woyw$>
*
ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S1047847724000078__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHDoPtQmQ$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S1047847724000078__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBSAzPhLw$>
*
Validation of electron-microscopy maps using solution small-angle X-ray scattering
https://urldefense.com/v3/__https://journals.iucr.org/d/issues/2024/07/00/wan5003/__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE_zO8WHw$ <https://urldefense.com/v3/__https://journals.iucr.org/d/issues/2024/07/00/wan5003/__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD8nQI45w$>
*
Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations
https://urldefense.com/v3/__https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2024.1393564/full__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE-IpKsKw$ <https://urldefense.com/v3/__https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2024.1393564/full__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBRcSL9zQ$>
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Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference
https://urldefense.com/v3/__https://journals.plos.org/ploscompbiol/article?id=10.1371*journal.pcbi.1012180__;Lw!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEAQuNnEw$ <https://urldefense.com/v3/__https://journals.plos.org/ploscompbiol/article?id=10.1371*journal.pcbi.1012180__;Lw!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCj0AevBA$>
*
Optimizing Contrast in Automated 4D STEM Cryotomography
https://urldefense.com/v3/__https://academic.oup.com/mam/article/30/3/476/7695190__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG7ejcWkA$ <https://urldefense.com/v3/__https://academic.oup.com/mam/article/30/3/476/7695190__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDe1igLHw$>
*
Cryo-tomography and 3D Electron Diffraction Reveal the Polar Habit and Chiral Structure of the Malaria Pigment Crystal Hemozoin
https://urldefense.com/v3/__https://pubs.acs.org/doi/10.1021/acscentsci.4c00162__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGJ12qlEw$ <https://urldefense.com/v3/__https://pubs.acs.org/doi/10.1021/acscentsci.4c00162__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA4UrdTUw$>
*
Reduction of SEM charging artefacts in native cryogenic biological samples
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.23.609373v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUENTKqqyw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.23.609373v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAWYUHKlw$>
*
EMhub: a web platform for data management and on-the-fly processing in scientific facilities
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.12.607607v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFYbpoqIg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.12.607607v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCewbcB5Q$>
Also, a follow-up to a topic I brought up a couple weeks ago about peer-reviewers directly discussing the paper and review with authors: someone asked which journals have allowed/disallowed this. Here are lists from my experience:
Allowed direct author-reviewer communication:
*
Acta Crystallographica Section D
*
Nature Communications
*
Biological Imaging
*
Cell Structure
Did not allow:
*
PNAS
*
IEEE Transactions on Medical Imaging
It might also depend on the editor.
Best wishes,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, August 19, 2024 3:07 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
New week, new papers and software:
(also, I'll include papers that I missed starting from June)
*
Cryo-electron microscopy in the study of virus entry and infection
https://urldefense.com/v3/__https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2024.1429180/full__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGo_acKcg$ <https://urldefense.com/v3/__https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2024.1429180/full__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAI9iJNEg$>
*
An image processing pipeline for electron cryo-tomography in RELION-5
https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1002/2211-5463.13873__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGiwdFbNw$ <https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1002/2211-5463.13873__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCs2TwBPw$>
*
JPEG Tomogram (reduce tomogram size by ~90% for visualization, annotation, sharing)
https://urldefense.com/v3/__https://github.com/alexjnoble/jpeg_tomogram__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEXAUDfCA$ <https://urldefense.com/v3/__https://github.com/alexjnoble/jpeg_tomogram__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaALwsyfVQ$>
*
A versatile correlative light and electron microscopy protocol for human brain and other biological models
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.11.598271v2__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG99GxZcA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.11.598271v2__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCVkhxFiw$>
*
The dynamic duo: cryo-EM teams up with machine learning to visualize biomolecules in motion
https://urldefense.com/v3/__https://www.tandfonline.com/doi/full/10.1080/07366205.2024.2355771__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFQQI4fyg$ <https://urldefense.com/v3/__https://www.tandfonline.com/doi/full/10.1080/07366205.2024.2355771__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBDNT2Pew$>
*
Determining Protein Secondary Structures in Heterogeneous Medium-Resolution Cryo-EM Images Using CryoSSESeg
https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acsomega.4c02608__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEnAR6soQ$ <https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acsomega.4c02608__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAixnEX4w$>
*
MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search
https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c02007__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEv9PW0Tw$ <https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c02007__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDlWgVfgg$>
Best wishes,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, August 12, 2024 10:54 AM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
New papers:
*
Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method
https://urldefense.com/v3/__https://www.nature.com/articles/s41598-024-68468-7__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEfMlmfSA$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41598-024-68468-7__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD5DciDFA$>
*
Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.04.606536v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGN2BSI2Q$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.04.606536v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCO1vCv5g$>
*
Tensorial template matching for fast cross-correlation with rotations and its application for tomography
https://urldefense.com/v3/__https://arxiv.org/abs/2408.02398__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEuJnp-4g$ <https://urldefense.com/v3/__https://arxiv.org/abs/2408.02398__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAAwp0z_Q$>
*
Multi-species cryoEM calibration and workflow verification standard
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.05.606612v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGOBvqDCw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.05.606612v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCBB7EyEQ$>
*
SPOT-RASTR—A cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface
https://urldefense.com/v3/__https://academic.oup.com/pnasnexus/article/3/8/pgae284/7727607__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG_8NEuYg$ <https://urldefense.com/v3/__https://academic.oup.com/pnasnexus/article/3/8/pgae284/7727607__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCO3bV5Hw$>
*
Smart parallel automated cryo-electron tomography
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02373-9__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHFUT1ejg$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02373-9__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBnJNUVQQ$>
*
DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02377-5__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEN5-rYHQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02377-5__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC9CtN65Q$>
*
Challenges, advances, and opportunities in RNA structural biology by Cryo-EM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24001210__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHsEyeehw$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24001210__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDN65Cy7g$>
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, August 5, 2024 3:50 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi cool people,
Below is this past week's installment of new cryoEM papers and related software - it was a slow week!
*
Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo
https://urldefense.com/v3/__https://www.cell.com/structure/fulltext/S0969-2126(24)00241-7__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGwuNk2Rg$ <https://urldefense.com/v3/__https://www.cell.com/structure/fulltext/S0969-2126(24)00241-7__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDvLw2SmA$>
*
Segment Anything Model 2 (SAM 2)
https://urldefense.com/v3/__https://ai.meta.com/sam2/__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEyPQ6U6w$ <https://urldefense.com/v3/__https://ai.meta.com/sam2/__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaChcmkS0A$>
Since it's a slow week, how about a discussion on cryoEM papers: Peer-review is a process that helps keep guard-rails on papers (which is good) but it also significantly slows down research compared to the computer science field, for example, which primarily uses preprints to rapidly increment progress. In contrast, it's common in my experience as an author and peer-reviewer for editors and reviewers to stymie progress in our field's development due to minor misunderstandings; e.g. a paper being rejected because a reviewer wrongly claims that a method is not novel and the editor accepting that claim.
To avoid many of these unnecessary issues, I decided late last year to only peer-review a paper if the editor allows for open discussion between myself and the authors by email (with the editor cc'ed). Have others used this method as well, or have another solution to this problem? Is this a problem?
Best wishes,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, July 29, 2024 9:39 AM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi cool people,
Below is this past week's installment of new cryoEM papers. There are many short M&M papers - they're not listed here for space reasons; the first link has a full list.
*
M&M papers:
https://urldefense.com/v3/__https://academic.oup.com/mam/issue/30/Supplement_1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF8cKfyfw$ <https://urldefense.com/v3/__https://academic.oup.com/mam/issue/30/Supplement_1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA8GsCcNw$>
*
Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.19.604374v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFcTPX_jA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.19.604374v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCGKf7ulg$>
*
Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.23.604154v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGHrO5Xrg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.23.604154v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD4MMdgkQ$>
*
Cryo-EM Screening of Apoferritin at 100 kV Using Hitachi’s HT7800 Thermionic Transmission Electron Microscope
https://urldefense.com/v3/__https://academic.oup.com/mam/article/30/Supplement_1/ozae044.379/7720487__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHmDfvqBg$ <https://urldefense.com/v3/__https://academic.oup.com/mam/article/30/Supplement_1/ozae044.379/7720487__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCc57boMw$>
*
All atom molecular dynamics simulations enable ensemble refinement of flexible and mismodelled cryo-EM derived RNA structures
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.24.604258v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFXHMb1FA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.24.604258v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA2fENYWQ$>
*
Likelihood-based interactive local docking into cryo-EM maps in ChimeraX
https://urldefense.com/v3/__https://journals.iucr.org/d/issues/2024/08/00/id5013/index.html__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHrEVNHgA$ <https://urldefense.com/v3/__https://journals.iucr.org/d/issues/2024/08/00/id5013/index.html__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC2zKGWog$>
Cheers,
Alex Noble
________________________________
From: Alex Noble <anoble at nysbc.org<mailto:anoble at nysbc.org>>
Sent: Monday, July 22, 2024 12:18 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: New cryoEM papers (#cryoem_papers)
Hi cool people,
Here is this past week's installment of new cryoEM papers (which will now also include new software):
*
MarkerDetector: A method for robust fiducial marker detection in electron micrographs using wavelet-based template
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1047847723001077__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEZ3WVjlg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1047847723001077__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCI0IBr8g$>
*
CryoEM Workflow Acceleration with Feret Signatures
https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/25/14/7593__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEIDUIjsg$ <https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/25/14/7593__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB_MBqN6g$>
*
St Jude's EMHub software for facility organization
https://urldefense.com/v3/__https://x.com/StJudeStructBio/status/1813236681388032326__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEy_e8KwQ$ <https://urldefense.com/v3/__https://x.com/StJudeStructBio/status/1813236681388032326__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBHPk25SQ$>
https://urldefense.com/v3/__https://github.com/3dem/emhub__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEBD2yo3A$ <https://urldefense.com/v3/__https://github.com/3dem/emhub__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA3pBRkNQ$>
*
CryoSamba: self-supervised deep volumetric denoising for cryo-electron tomography data
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.11.603117v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF2WLflPg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.11.603117v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD423GFGg$>
*
Denoising, Deblurring, and optical Deconvolution for cryo-ET and light microscopy with a physics-informed deep neural network DeBCR
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603278v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG4MR98QA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603278v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaARuc_hDw$>
*
Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.15.603622v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG5AA9lJw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.15.603622v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAwb6Y3iA$>
*
Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0304399123001997__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFncX5x6A$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0304399123001997__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAujrEzPg$>
*
CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02340-4__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG9TEeC9w$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02340-4__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDmTIMSJA$>
*
Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
https://urldefense.com/v3/__https://app.jove.com/b/66310/modeling-small-molecule-ligands-in-cryoem-maps-of-macromolecules__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF6pwkDrg$ <https://urldefense.com/v3/__https://app.jove.com/b/66310/modeling-small-molecule-ligands-in-cryoem-maps-of-macromolecules__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAZVl7WNg$>
*
AQuaRef: Machine learning accelerated quantum refinement of protein structures
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.21.604493v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGNDqZKNg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.21.604493v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDTCYM-jg$>
*
The myth of high-resolution liquid phase biological electron microscopy
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/pro.5125__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGIJKgrTw$ <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/pro.5125__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB8q7WNuQ$>
Best wishes,
Alex Noble
________________________________
From: Alex Noble
Sent: Monday, July 15, 2024 2:39 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: New cryoEM papers (#cryoem_papers)
Hi cool people,
I've been finding new cryoEM papers that are interesting to me (methods/new tech, machine learning, cryoFIB/SEM-ET, etc.; typically no biology-focused papers) for our internal Slack channel for years and decided to share them with the community as well. Many papers fall through the cracks, so I think it would be good to have the whole cryoEM community on the same page. Hopefully it will make the community more productive and speed up the pace of developments.=)
There used to be a twitter bot that (@cryoem_papers<https://urldefense.com/v3/__https://x.com/cryoem_papers__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAYWXYivw$>) that did this work. I'll add #cryoem_papers to this recurrent email so it's easy for you to filter them as you wish.
I'll aim to post new papers every Monday. Here's the first batch covering the past 2 weeks:
*
CryoViT: Efficient Segmentation of Cryogenic Electron Tomograms with Vision Foundation Models
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.26.600701v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUHndYQv3w$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.26.600701v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB9qiFFww$>
*
Accurate size-based protein localization from cryo-ET tomograms
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF1zmOAGg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBqssocIw$>
*
Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49858-x__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEbCIotvA$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49858-x__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC_8lNtVg$>
*
OPUS-TOMO: Deep Learning Framework for Structural Heterogeneity Analysis in Cryo-electron Tomography
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE6UYgDQA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBvor0u6A$>
*
Frontiers in integrative structural biology: modeling disordered proteins and utilizing in situ data
https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGpldQjGg$ <https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDDrwBjoQ$>
*
Direct Measurement of the Critical Cooling Rate for the Vitrification of Water
https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGoFJMvhA$ <https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB1WLcPsw$>
*
DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map
https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGWthuOIA$ <https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC8ivCNKg$>
*
Einstein from Noise: Statistical Analysis
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEz77HsZA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCXP26HYA$>
*
Advances in cryo-ET data processing: meeting the demands of visual proteomics
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000885__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGYkJptdg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000885__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaCNbyOPbQ$>
*
Expanding insights from in situ cryo-EM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEIgMiMmA$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaB3QyUenw$>
*
High-resolution real-space reconstruction of cryo-EM structures using a neural field network
https://urldefense.com/v3/__https://www.nature.com/articles/s42256-024-00870-2__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFq_44aCQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s42256-024-00870-2__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaD-3J6Z1g$>
*
Nanobody-assisted cryoEM structural determination for challenging proteins
https://urldefense.com/v3/__https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(24)00136-1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUG0F5LijA$ <https://urldefense.com/v3/__https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(24)00136-1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDvjKipVQ$>
*
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49647-6__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFPZMgMCg$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49647-6__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAQl44cyw$>
*
Training-free CryoET Tomogram Segmentation
https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGpoTB0UQ$ <https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAX5mvRyw$>
*
Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference
https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGVDDVAEw$ <https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaC7t7efpQ$>
*
CryoJAM: Automating Protein Homolog Fitting in Medium Resolution Cryo-EM Density Maps
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.10.602952v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUF-gsM-Iw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.10.602952v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDZEweLqw$>
*
Ais: streamlining segmentation of cryo-electron tomography datasets
https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGPdVR8gQ$ <https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAZP1ppMw$>
*
Cryo-electron tomography pipeline for plasma membranes
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGBNn4kAw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaDXkGtryw$>
*
DeepOrientation: Deep Orientation Estimation of Macromolecules in Cryo-electron tomography
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603241v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUE6WonhqA$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603241v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAryrG6cg$>
*
Graphene in cryo-EM specimen optimization
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUGMcGw3-g$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBNaPZH4g$>
*
FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer
https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUFYK3D_tA$ <https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaA71U48DA$>
*
Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling
https://urldefense.com/v3/__https://arxiv.org/abs/2406.18610__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEv-0XcxQ$ <https://urldefense.com/v3/__https://arxiv.org/abs/2406.18610__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBgQfYlog$>
*
Visualizing the translation landscape in human cells at high resolution
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1__;!!Mih3wA!FqRgmKkM4aqZ5rx_1dToio3WndUtZjD9IwFjyZVxGLCv8w07MmQR_tSqfdLaacYvIo3AOOWLssT1xvxrwUEabc71qg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaAFLe82eA$>
Best wishes,
-Alex Noble
SEMC/NYSBC
X: @alexjamesnoble<https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!BfIZdvWqu6yQ1rVcCSy39El7_NKPjyEdE-em8YqUnf3y_At9IAvBAzXF3VyZ6O0zUavfIhxLWaBzOyN3ng$>
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