Literature DB >> 31394387

Modelling structures in cryo-EM maps.

Sony Malhotra1, Sylvain Träger2, Matteo Dal Peraro2, Maya Topf3.   

Abstract

Recent advances in structure determination of sub-cellular structures using cryo-electron microscopy and tomography have enabled us to understand their architecture in a more detailed manner and gain insight into their function. The choice of approach to use for atomic model building, fitting, refinement and validation in the 3D map resulting from these experiments depends primarily on the resolution of the map and the prior information on the corresponding model. Here, we survey some of such methods and approaches and highlight their uses in specific recent examples.
Copyright © 2019 Elsevier Ltd. All rights reserved.

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Year:  2019        PMID: 31394387     DOI: 10.1016/j.sbi.2019.05.024

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  18 in total

1.  Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps.

Authors:  Doo Nam Kim; Dominik Gront; Karissa Y Sanbonmatsu
Journal:  J Chem Inf Model       Date:  2020-05-18       Impact factor: 4.956

Review 2.  Integrative structural modeling of macromolecular complexes using Assembline.

Authors:  Vasileios Rantos; Kai Karius; Jan Kosinski
Journal:  Nat Protoc       Date:  2021-11-29       Impact factor: 13.491

3.  Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.

Authors:  Eman Alnabati; Genki Terashi; Daisuke Kihara
Journal:  Curr Protoc       Date:  2022-07

4.  Computational models in the service of X-ray and cryo-electron microscopy structure determination.

Authors:  Andriy Kryshtafovych; John Moult; Reinhard Albrecht; Geoffrey A Chang; Kinlin Chao; Alec Fraser; Julia Greenfield; Marcus D Hartmann; Osnat Herzberg; Inokentijs Josts; Petr G Leiman; Sara B Linden; Andrei N Lupas; Daniel C Nelson; Steven D Rees; Xiaoran Shang; Maria L Sokolova; Henning Tidow
Journal:  Proteins       Date:  2021-09-06

5.  Triangulating variation in the population to define mechanisms for precision management of genetic disease.

Authors:  Chao Wang; Frédéric Anglès; William E Balch
Journal:  Structure       Date:  2022-06-16       Impact factor: 5.871

6.  LPTD: a novel linear programming-based topology determination method for cryo-EM maps.

Authors:  Bahareh Behkamal; Mahmoud Naghibzadeh; Andrea Pagnani; Mohammad Reza Saberi; Kamal Al Nasr
Journal:  Bioinformatics       Date:  2022-05-13       Impact factor: 6.931

Review 7.  Cryo-electron Microscopy of Adeno-associated Virus.

Authors:  Scott M Stagg; Craig Yoshioka; Omar Davulcu; Michael S Chapman
Journal:  Chem Rev       Date:  2022-05-16       Impact factor: 72.087

8.  A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps.

Authors:  Biao Zhang; Xi Zhang; Robin Pearce; Hong-Bin Shen; Yang Zhang
Journal:  J Mol Biol       Date:  2020-08-06       Impact factor: 5.469

9.  CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles.

Authors:  Sylvain Träger; Giorgio Tamò; Deniz Aydin; Giulia Fonti; Martina Audagnotto; Matteo Dal Peraro
Journal:  Bioinformatics       Date:  2021-05-17       Impact factor: 6.937

10.  Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.

Authors:  Takaharu Mori; Genki Terashi; Daisuke Matsuoka; Daisuke Kihara; Yuji Sugita
Journal:  J Chem Inf Model       Date:  2021-06-18       Impact factor: 6.162

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