Journal Article

PUBDB-2023-08078

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Integrating model simulation tools and cryo‐electron microscopy

Beton, J.CSSB* ; Cragnolini, T.CSSB* ; Kaleel, M.Extern*CSSB* ; Mulvaney, T.CSSB* ; Sweeney, A.CSSB* ; Topf, M. (Corresponding author)Extern*CSSB*

2023
Wiley-Blackwell Malden, MA

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Please use a persistent id in citations: doi:10.1002/wcms.1642  doi:10.3204/PUBDB-2023-08078

Abstract: The power of computer simulations, including machine-learning, has become an inseparable part of scientific analysis of biological data. This has significantly impacted the field of cryogenic electron microscopy (cryo-EM), which has grown dramatically since the “resolution-revolution.” Many maps are now solved at 3–4 Å or better resolution, although a significant proportion of maps deposited in the Electron Microscopy Data Bank are still at lower resolution, where the positions of atoms cannot be determined unambiguously. Additionally, cryo-EM maps are often characterized by a varying local resolution, partly due to conformational heterogeneity of the imaged molecule. To address such problems, many computational methods have been developed for cryo-EM map reconstruction and atomistic model building. Here, we review the development in algorithms and tools for building models in cryo-EM maps at different resolutions. We describe methods for model building, including rigid and flexible fitting of known models, model validation, small-molecule fitting, and model visualization. We provide examples of how these methods have been used to elucidate the structure and function of dynamic macromolecular machines.This article is categorized under: Structure and Mechanism > Molecular Structures Structure and Mechanism > Computational Biochemistry and Biophysics Software > Molecular Modeling

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Contributing Institute(s):

1. CSSB - Leibniz-Institut für Experimentelle Virologie (LIV) / UKE - Maya Topf (CSSB-LIV/UKE-MT)

Research Program(s):

1. 899 - ohne Topic (POF4-899) (POF4-899)

Experiment(s):

1. No specific instrument

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Database coverage:
; ; ; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; DEAL Wiley ; Essential Science Indicators ; IF >= 10 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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