[3dem] New cryoEM papers (#cryoem_papers)
Alex Noble
anoble at nysbc.org
Mon Aug 12 07:54:52 PDT 2024
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClz1vQVn6A$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzA4k6mrg$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwfk41vag$
*
Multi-species cryoEM calibration and workflow verification standard
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.05.606612v1__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwkxoSNWw$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClw18IDGhg$
*
Smart parallel automated cryo-electron tomography
https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02373-9__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzJtpHauA$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzlTJaFdA$
*
Challenges, advances, and opportunities in RNA structural biology by Cryo-EM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24001210__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaCly6J-2EQg$
________________________________
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxkc3ExZQ$
*
Segment Anything Model 2 (SAM 2)
https://urldefense.com/v3/__https://ai.meta.com/sam2/__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwte2fKug$
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxF7b8BuQ$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClyJTgRANQ$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxcLrC1Rg$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzHTdnmpQ$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClx82ExCwg$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClz3x4xiBg$
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClyV0VVKkQ$
*
CryoEM Workflow Acceleration with Feret Signatures
https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/25/14/7593__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClyYAoW_iA$
*
St Jude's EMHub software for facility organization
https://urldefense.com/v3/__https://x.com/StJudeStructBio/status/1813236681388032326__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzlzfVF3g$
https://urldefense.com/v3/__https://github.com/3dem/emhub__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxoM2zULw$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxF89vMLA$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClyaS3gM-w$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaCly5s2_sLA$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClx8xh4bbQ$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwWofxddA$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwFrQPi8A$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzpWxQd3A$
*
The myth of high-resolution liquid phase biological electron microscopy
https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/pro.5125__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClyQbZw0ag$
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzGmD-XVQ$ >) 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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxhEwU91Q$
*
Accurate size-based protein localization from cryo-ET tomograms
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxQGt2I0Q$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClz_1s6Vfg$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxWPF4qUQ$
*
Frontiers in integrative structural biology: modeling disordered proteins and utilizing in situ data
https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClyMorr0Hg$
*
Direct Measurement of the Critical Cooling Rate for the Vitrification of Water
https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwSvNqbJQ$
*
DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map
https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwvmfuIgA$
*
Einstein from Noise: Statistical Analysis
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaCly3pV8GVw$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwtbE7GBg$
*
Expanding insights from in situ cryo-EM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClyc2Zf2-w$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClyTKkq2bA$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzuRh1s0w$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClz7y_PzTw$
*
Training-free CryoET Tomogram Segmentation
https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwtnvQ3BQ$
*
Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference
https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClzrJ-81Yw$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwAK7SFKQ$
*
Ais: streamlining segmentation of cryo-electron tomography datasets
https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClz7wzoh5A$
*
Cryo-electron tomography pipeline for plasma membranes
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxPe4Gvow$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClxJUOpKBQ$
*
Graphene in cryo-EM specimen optimization
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClz6yHNeYg$
*
FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer
https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwjVdShpg$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwFzX45Tg$
*
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!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClwaad8qCw$
Best wishes,
-Alex Noble
SEMC/NYSBC
X: @alexjamesnoble<https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!G-FYE_r8ME6oRYfwcrk6pcQaMIMWXQTfF0yasvUzx-BnSnR_Tbawob-uRE1qDafh-PFg4XTaClz7rzip9w$ >
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