[3dem] New cryoEM papers (#cryoem_papers)
Alex Noble
anoble at nysbc.org
Mon Sep 23 14:11:14 PDT 2024
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz0eEc87w$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czUmcP0Eg$
*
The future of integrated structural biology
https://urldefense.com/v3/__https://www.cell.com/structure/fulltext/S0969-2126(24)00331-9__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czDfQQDSQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czGQ1TX3A$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyA8XMpZQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw3k8WnVA$
*
How to autocontouring grid squares in SerialEM:
https://urldefense.com/v3/__https://x.com/Nexperion/status/1836681264499139055__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwtaygfMg$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czJVyxPwA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwa2-HZcA$
*
Outlier Removal in Cryo-EM via Radial Profiles
https://urldefense.com/v3/__https://arxiv.org/abs/2409.05523__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw9uSyiYw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxKID4dpA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxofkyVRg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxQutqTiQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cybCnf6wQ$
*
Single-Particle Cryo-EM: What happens inside the Black Box?
https://urldefense.com/v3/__https://osf.io/preprints/osf/5empt__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz8JSpgTw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyIu1P5xg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwVXg3mmw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwsgJTfFw$
*
Evaluating Cryo-TEM Reconstruction Accuracy of Self-Assembled Polymer Nanostructures
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/marc.202400589__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cx-9F4fzQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyDYq3Wig$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz5PF0q_g$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwX1i26RA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyRFic4VA$
*
Academic Journal Publishers Antitrust Litigation
https://urldefense.com/v3/__https://www.lieffcabraser.com/antitrust/academic-journals/__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz2OTFxNA$
"... 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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwh0UBwVg$
https://urldefense.com/v3/__https://x.com/DawidZyla/status/1835077103630664087__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz8wGw4qg$ <https://urldefense.com/v3/__https://x.com/DawidZyla/status/1835077103630664087?s=19__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxxSS2DgQ$ >
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz9v8a2GA$
https://urldefense.com/v3/__https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwMrDK8ZA$
https://urldefense.com/v3/__https://paddlehelix.baidu.com/__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw5PRGnUg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw99a29sA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyZnpmh_w$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyqsCpQXQ$
*
Teaching protein structure and function through molecular visualization
https://urldefense.com/v3/__https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.21860__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyYE76kfw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz8fWpaCA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwkvspHKg$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyZBUTdXw$
*
Deep Mapper: Efficient Visualization of Plausible Conformational Pathways
https://urldefense.com/v3/__https://arxiv.org/abs/2402.19177__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxUIy_TUA$
*
Liquid Phase Electron Microscopy of Bacterial Ultrastructure
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202402871__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czIXa9Elg$
*
Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE
https://urldefense.com/v3/__https://elifesciences.org/articles/99702__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyS5mOQNw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxGjlMLZg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxO1UjCzg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwtHjF7MA$
*
Cryo-Electron Microscopy Studies of Biomolecular Structure and Dynamics
https://urldefense.com/v3/__https://www.mdpi.com/2072-666X/15/9/1092__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cy0DtrcDQ$
*
AlphaFold3 Open-Source Implementation
https://urldefense.com/v3/__https://github.com/Ligo-Biosciences/AlphaFold3__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cygIMt0nQ$
https://urldefense.com/v3/__https://x.com/ArdaGoreci/status/1830744265007480934__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cweoiuoiA$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz1AGg-eA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwQ7Oe2cA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czQGLbJBw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz13bLq5w$
*
Ligand Identification using Deep Learning
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.27.610022v1__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz-2VDfZA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cymM0rdyA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cywvApE0g$
*
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding
https://urldefense.com/v3/__https://arxiv.org/abs/2408.11363__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czQvGljWA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwJYpmuSw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwG6tNSyA$
*
Wiggle for UCSF ChimeraX
https://urldefense.com/v3/__https://x.com/bj_charles/status/1567346827456028673__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czXKmz1aw$
https://urldefense.com/v3/__https://github.com/charbj/wiggle__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxHyjazzQ$
*
maskChains for ChimeraX
https://urldefense.com/v3/__https://x.com/JiangLabCryoEM/status/1828861099485073537__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwrqqTstA$
*
Technical Report of HelixFold3 for Biomolecular Structure Prediction
https://urldefense.com/v3/__https://arxiv.org/abs/2408.16975__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz9v8a2GA$
https://urldefense.com/v3/__https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwMrDK8ZA$
https://urldefense.com/v3/__https://paddlehelix.baidu.com/?redirect__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czhVIXn4A$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cybRImtMA$
*
Generative artificial intelligence performs rudimentary structural biology modeling
https://urldefense.com/v3/__https://www.nature.com/articles/s41598-024-69021-2__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyEx3azmg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwmIwOM9A$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyK65E-6A$
*
CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM
https://urldefense.com/v3/__https://arxiv.org/abs/2408.05526__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwpDzOH0w$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czsZqCEvw$
*
Correlative cryo-microscopy pipelines for in situ cellular studies
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000694__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwj7BmqgQ$
*
Building a super-resolution fluorescence cryomicroscope
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000578__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwpoyVbvw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxaFEbE8A$
*
Toward quantitative super-resolution methods for cryo-CLEM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0091679X24000591__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwOSskphw$
*
Recent Technical Advances in Cellular Cryo-Electron Tomography
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1357272524001407__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxD6eJEpQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyw97IGeg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwlpbHygA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czDKChMBg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyoj2jeww$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxbHnMqMw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czFghIdeg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwTVIR0SQ$
*
Optimizing Contrast in Automated 4D STEM Cryotomography
https://urldefense.com/v3/__https://academic.oup.com/mam/article/30/3/476/7695190__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwqy_XwVQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyBEjVWQA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw45ebV_g$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czc33aO6A$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwNEp7-XA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyioq5O5Q$
*
JPEG Tomogram (reduce tomogram size by ~90% for visualization, annotation, sharing)
https://urldefense.com/v3/__https://github.com/alexjnoble/jpeg_tomogram__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxxNweQDQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czimhg_hg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cysG2FSUA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czfeg0nnQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cz5CGZ_aA$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cy35HqyRQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxb9nrMKg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czLWlBY_w$
*
Multi-species cryoEM calibration and workflow verification standard
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.05.606612v1__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxZBRSaeA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyXgBY_aQ$
*
Smart parallel automated cryo-electron tomography
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02373-9__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyIsIv6bA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyLxSxX1g$
*
Challenges, advances, and opportunities in RNA structural biology by Cryo-EM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24001210__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwbRcroJQ$
________________________________
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw1jHh4mQ$
*
Segment Anything Model 2 (SAM 2)
https://urldefense.com/v3/__https://ai.meta.com/sam2/__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyVZiUnHA$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czA0QJd3Q$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cweRLgDOg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxngYLmvQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czWAfSjIQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxGnRrkBQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxzyfb-RQ$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyqExxyyg$
*
CryoEM Workflow Acceleration with Feret Signatures
https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/25/14/7593__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw2i5aP1Q$
*
St Jude's EMHub software for facility organization
https://urldefense.com/v3/__https://x.com/StJudeStructBio/status/1813236681388032326__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cx04FfcOQ$
https://urldefense.com/v3/__https://github.com/3dem/emhub__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cy4coLfIg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw2W8nTOQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxYi7umKA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxWZd9VUw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwG8WMPyw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyhyITDOA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyirLWPXg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cw0gSITGg$
*
The myth of high-resolution liquid phase biological electron microscopy
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/pro.5125__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxW21pK9A$
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cx6RBmvLg$ >) 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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwyQVZB8g$
*
Accurate size-based protein localization from cryo-ET tomograms
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czAJ7Gm3g$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czUpgrqTg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwjXX5D7g$
*
Frontiers in integrative structural biology: modeling disordered proteins and utilizing in situ data
https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwuURm4Gw$
*
Direct Measurement of the Critical Cooling Rate for the Vitrification of Water
https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czWsj-Opg$
*
DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map
https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czVlGL6aA$
*
Einstein from Noise: Statistical Analysis
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxPB9gDeQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwz_goTKg$
*
Expanding insights from in situ cryo-EM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyB9AnSzg$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxzZYRniw$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cy-g8bO1g$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwErA0d8w$
*
Training-free CryoET Tomogram Segmentation
https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cyUcju93A$
*
Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference
https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cxDND18DQ$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwM6dTzQg$
*
Ais: streamlining segmentation of cryo-electron tomography datasets
https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cy0_yqM_A$
*
Cryo-electron tomography pipeline for plasma membranes
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cy9oDlqcA$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cytKc04Og$
*
Graphene in cryo-EM specimen optimization
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwWW0Fy-g$
*
FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer
https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwPo8zj2g$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6cwXvfWvww$
*
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!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czMVggm8w$
Best wishes,
-Alex Noble
SEMC/NYSBC
X: @alexjamesnoble<https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!HDJvsNNGoYLCV7f825hxFXvvQocbynDsR4r2QF0fqSnByxWphqDFSWOQ3gwLc7jlnXdxQHgB6czU-A2a8w$ >
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