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Cryo-RALib – a modular library for accelerating alignment in cryo-EM [article]

Szu-Chi Chung, Cheng-Yu Hung, Huei-Lun Siao, Hung-Yi Wu, Wei-Hau Chang, I-Ping Tu
2021 arXiv   pre-print
Thanks to automated cryo-EM and GPU-accelerated processing, single-particle cryo-EM has become a rapid structure determination method that permits capture of dynamical structures of molecules in solution  ...  In addition, we connect the cryo-EM image analysis with the python data science stack so as to make it easier for users to perform data analysis and visualization.  ...  Acknowledgement The authors gratefully acknowledge Ryan Jeng from Nvidia and the NCHC GPU Hackathon for the help on our research project.  ... 
arXiv:2011.05755v4 fatcat:gtagsscxlbfehetvrp7aff5hsm

Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes

Boon Chong Goh, Jodi A. Hadden, Rafael C. Bernardi, Abhishek Singharoy, Ryan McGreevy, Till Rudack, C. Keith Cassidy, Klaus Schulten
2016 Annual Review of Biophysics  
The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems.  ...  The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed.  ...  Phillips for insightful discussions that contributed to this review, as well as Bo Liu for kindly providing a ribosome figure.  ... 
doi:10.1146/annurev-biophys-062215-011113 pmid:27145875 pmcid:PMC5526348 fatcat:rrcwq75t7rc6jbyg5etr44mzbe

Insights into the Structure of Amyloid Fibrils

Karen E. Marshall, Louise C. Serpell
2009 The Open Biology Journal  
Structural characterisation of these fibres is limited by their insoluble and heterogeneous nature.  ...  and macromolecular structure to the atomic interactions that promote assembly and stabilise the amyloid core.  ...  Julian Thorpe for valuable technical support for the electron microscope and Kyle Morris, Dr. Thomas Williams and Dr. Violetta Soura for useful discussions and help.  ... 
doi:10.2174/1874196700902010185 fatcat:rd4vt2jkzfhfrloerv2ksthc7e

Accelerated Cryo-EM Structure Determination with Parallelisation using GPUs in Relion-2

Dari Kimanius, Björn Forsberg, Erik Lindahl
2017 Biophysical Journal  
By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology.  ...  This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.  ...  ; and Toby Darling, Jake Grimmett, and Stefan Fleichmann for technical support.  ... 
doi:10.1016/j.bpj.2016.11.3096 fatcat:efrh6nreazgcbdl5nzxhnh2kyi

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

Dari Kimanius, Björn O Forsberg, Sjors HW Scheres, Erik Lindahl
2016 eLife  
By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology.  ...  This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.  ...  ; and Toby Darling, Jake Grimmett, and Stefan Fleichmann for technical support.  ... 
doi:10.7554/elife.18722 pmid:27845625 pmcid:PMC5310839 fatcat:v4tx5lc3snd5the6ojfzwdrxpq

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 [article]

Dari Kimanius, Bjorn O Forsberg, Sjors Scheres, Erik Lindahl
2016 biorxiv/medrxiv   pre-print
By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming struc- tural biology.  ...  This enables high-resolution cryo-EM struc- ture determination in a matter of days on a single workstation.  ...  ; and Toby Darling, Jake Grimmett, and Stefan Fleichmann for technical support.  ... 
doi:10.1101/059717 fatcat:ddcvkwtlj5azpjfaeypn2gyqii

Electron cryomicroscopy as a powerful tool in biomedical research

Dennis Quentin, Stefan Raunser
2018 Journal of Molecular Medicine  
Consequently, it has become the focus of attention for structure-based drug design. In this review, we describe the basics of cryo-EM and highlight its growing role in biomedical research.  ...  Facilitated by recent technological breakthroughs, the Nobel prize-winning technique electron cryomicroscopy (cryo-EM) has become a versatile and extremely powerful tool to solve routinely near-atomic  ...  Gonen for kindly providing the diffraction image depicted in Fig. 1 .  ... 
doi:10.1007/s00109-018-1640-y pmid:29730699 pmcid:PMC5988769 fatcat:tzmleiw7ufcpbkyhor4bf3b5ci

AITom: Open-source AI platform for cryo-electron tomography data analysis [article]

Xiangrui Zeng, Min Xu
2020 arXiv   pre-print
Tomograms captured by cryo-ET contain heterogeneous structures representing the complex and dynamic subcellular environment.  ...  However, the systematic localization, identification, segmentation, and structural recovery of the subcellular components require efficient and accurate large-scale image analysis methods.  ...  on large scale supervised video datasets.  ... 
arXiv:1911.03044v2 fatcat:445x3wnfafevxm6jdiqt27khhu

Cryo-EM of amyloid fibrils and cellular aggregates

Anthony WP Fitzpatrick, Helen R Saibil
2019 Current Opinion in Structural Biology  
In this review, we illustrate the contributions of cryo-EM and related methods to the structure determination of amyloid fibrils extracted post mortem from patient brains or formed in vitro.  ...  Large deposits of amyloid fibrils are typically associated with cell death in late stage pathology.  ...  Acknowledgements We thank Tom Peskett for helpful comments on the manuscript. This work was supported by Wellcome Trust grant 106252/Z/14/Z to H.R.S and N.I.H. grant U01NS110438 to A.W.P.F.  ... 
doi:10.1016/j.sbi.2019.05.003 pmid:31200186 pmcid:PMC6778506 fatcat:jophukftvbfdxmssxqjmcgho2u

Parallel, distributed and GPU computing technologies in single-particle electron microscopy

Martin Schmeisser, Burkhard C. Heisen, Mario Luettich, Boris Busche, Florian Hauer, Tobias Koske, Karl-Heinz Knauber, Holger Stark
2009 Acta Crystallographica Section D: Biological Crystallography  
Most known methods for the determination of the structure of macromolecular complexes are limited or at least restricted at some point by their computational demands.  ...  Recent developments in information technology such as multicore, parallel and GPU processing can be used to overcome these limitations.  ...  Additionally, we would like to thank everyone who runs the SmartTray on their computer.  ... 
doi:10.1107/s0907444909011433 pmid:19564686 pmcid:PMC2703572 fatcat:puw6niofz5au3fzybp7fn7tjxa

Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC

Eric Wright, Mauricio Ferrato, Alexander J. Bryer, Robert Searles, Juan R. Perilla, Sunita Chandrasekaran, Dina Schneidman-Duhovny
2020 PLoS Computational Biology  
However, structure determination of large complexes and assemblies based on NMR data alone remains challenging due to the complexity of the calculations.  ...  Here, we present a hardware accelerated strategy for the estimation of NMR chemical-shifts of large macromolecular complexes based on the previously published PPM_One software.  ...  Cryo-EM of the dynamin polymer assembled on lipid membrane.  ... 
doi:10.1371/journal.pcbi.1007877 pmid:32401799 fatcat:7u6wwfmi6rcexlmt6jumjcof7e

Cryo-EM of dynamic protein complexes in eukaryotic DNA replication

Jingchuan Sun, Zuanning Yuan, Lin Bai, Huilin Li
2016 Protein Science  
Some of these proteins form stable complexes that are amenable to high-resolution structure determination by cryo-EM, thanks to the recent advent of the direct electron detector and powerful image analysis  ...  It is often necessary to positively identify the feature-of-interest in a low resolution EM structure.  ...  Acknowledgments The EM work described here on yeast DNA replication initiation was in collaboration with Bruce Stillman Lab at Cold Spring Harbor Laboratory and Christian Speck Lab at Imperial College  ... 
doi:10.1002/pro.3033 pmid:27589669 pmcid:PMC5192969 fatcat:qh7la4y5kve5foe44jjlb4d7um

Role of integrative structural biology in understanding transcriptional initiation

Michael J. Trnka, Riccardo Pellarin, Philip J. Robinson
2019 Methods  
and compositional heterogeneity.  ...  Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest.  ...  Even though cryo-EM has advanced significantly, heterogeneity derived from non-discrete, continual motions of domains still provides a significant challenge to algorithms designed to classify particles  ... 
doi:10.1016/j.ymeth.2019.03.009 pmid:30890443 pmcid:PMC6617507 fatcat:pgdbipcqmbfzdmqhg22fzs6hsy

Structural Insights into the Eukaryotic Transcription Initiation Machinery

Eva Nogales, Robert K. Louder, Yuan He
2017 Annual Review of Biophysics  
In the last few years, however, progress in cryo-electron microscopy (cryo-EM) has made possible the visualization, at increasingly better resolution, of large PIC assemblies in different functional states  ...  These structures can now be interpreted in near-atomic detail and provide an exciting structural framework for past and future functional studies, giving us unique mechanistic insight into the complex  ...  Our emphasis is on large components of the PIC that for many years remained highly challenging for structural studies.  ... 
doi:10.1146/annurev-biophys-070816-033751 pmid:28532216 pmcid:PMC6186020 fatcat:djuol6yj35bzxjpm3uugopr7zm

TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis

Zachary Frazier, Min Xu, Frank Alber
2017 Structure  
This paper introduces an open source software platform, TomoMiner, for large-scale subtomogram classification, template matching, subtomogram averaging, and alignment.  ...  Often, these subtomograms represent a heterogeneous sample due to variations in structure and composition of a complex in situ form or because particles are a mixture of different complexes.  ...  Acknowledgments We thank Long Pei for his contributions and suggestions. We thank Dr. Martin Beck for sharing code for simulating subtomograms. We thank Dr.  ... 
doi:10.1016/j.str.2017.04.016 pmid:28552576 pmcid:PMC5567730 fatcat:dbw6awqaazairlhdhtzpw5rcfy
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