Literature DB >> 31576602

Cryo-electron microscopy targets in CASP13: Overview and evaluation of results.

Andriy Kryshtafovych1, Sony Malhotra2, Bohdan Monastyrskyy1, Tristan Cragnolini2, Agnel-Praveen Joseph2, Wah Chiu3, Maya Topf2.   

Abstract

Structures of seven CASP13 targets were determined using cryo-electron microscopy (cryo-EM) technique with resolution between 3.0 and 4.0 Å. We provide an overview of the experimentally derived structures and describe results of the numerical evaluation of the submitted models. The evaluation is carried out by comparing coordinates of models to those of reference structures (CASP-style evaluation), as well as checking goodness-of-fit of modeled structures to the cryo-EM density maps. The performance of contributing research groups in the CASP-style evaluation is measured in terms of backbone accuracy, all-atom local geometry and similarity of inter-subunit interfaces. The results on the cryo-EM targets are compared with those on the whole set of eighty CASP13 targets. A posteriori refinement of the best models in their corresponding cryo-EM density maps resulted in structures that are very close to the reference structure, including some regions with better fit to the density.
© 2019 Wiley Periodicals, Inc.

Entities:  

Keywords:  CASP; cryo-EM; electron microscopy; model evaluation; protein structure prediction

Mesh:

Substances:

Year:  2019        PMID: 31576602      PMCID: PMC7197460          DOI: 10.1002/prot.25817

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  26 in total

1.  An automatic method for CASP9 free modeling structure prediction assessment.

Authors:  Qian Cong; Lisa N Kinch; Jimin Pei; Shuoyong Shi; Vyacheslav N Grishin; Wenlin Li; Nick V Grishin
Journal:  Bioinformatics       Date:  2011-10-12       Impact factor: 6.937

2.  Scoring functions for cryoEM density fitting.

Authors:  Daven Vasishtan; Maya Topf
Journal:  J Struct Biol       Date:  2011-02-04       Impact factor: 2.867

3.  Comparative analysis of methods for evaluation of protein models against native structures.

Authors:  Kliment Olechnovič; Bohdan Monastyrskyy; Andriy Kryshtafovych; Česlovas Venclovas
Journal:  Bioinformatics       Date:  2019-03-15       Impact factor: 6.937

4.  Evaluation of the template-based modeling in CASP12.

Authors:  Andriy Kryshtafovych; Bohdan Monastyrskyy; Krzysztof Fidelis; John Moult; Torsten Schwede; Anna Tramontano
Journal:  Proteins       Date:  2017-12-04

5.  Assessment of protein assembly prediction in CASP12.

Authors:  Aleix Lafita; Spencer Bliven; Andriy Kryshtafovych; Martino Bertoni; Bohdan Monastyrskyy; Jose M Duarte; Torsten Schwede; Guido Capitani
Journal:  Proteins       Date:  2017-11-08

6.  Evaluation system and web infrastructure for the second cryo-EM model challenge.

Authors:  Andriy Kryshtafovych; Paul D Adams; Catherine L Lawson; Wah Chiu
Journal:  J Struct Biol       Date:  2018-07-12       Impact factor: 2.867

7.  Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge.

Authors:  Andriy Kryshtafovych; Bohdan Monastyrskyy; Paul D Adams; Catherine L Lawson; Wah Chiu
Journal:  Data Brief       Date:  2018-09-08

8.  New tools for the analysis and validation of cryo-EM maps and atomic models.

Authors:  Pavel V Afonine; Bruno P Klaholz; Nigel W Moriarty; Billy K Poon; Oleg V Sobolev; Thomas C Terwilliger; Paul D Adams; Alexandre Urzhumtsev
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-09-03       Impact factor: 7.652

9.  lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.

Authors:  Valerio Mariani; Marco Biasini; Alessandro Barbato; Torsten Schwede
Journal:  Bioinformatics       Date:  2013-08-27       Impact factor: 6.937

10.  Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment.

Authors:  Agnel Praveen Joseph; Sony Malhotra; Tom Burnley; Chris Wood; Daniel K Clare; Martyn Winn; Maya Topf
Journal:  Methods       Date:  2016-03-14       Impact factor: 3.608

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  11 in total

Review 1.  Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps.

Authors:  Tristan Cragnolini; Aaron Sweeney; Maya Topf
Journal:  Methods Mol Biol       Date:  2021

2.  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

3.  Cryo-EM targets in CASP14.

Authors:  Tristan Cragnolini; Andriy Kryshtafovych; Maya Topf
Journal:  Proteins       Date:  2021-09-16

4.  Critical assessment of methods of protein structure prediction (CASP)-Round XIII.

Authors:  Andriy Kryshtafovych; Torsten Schwede; Maya Topf; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2019-10-23

5.  Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

Authors:  Catherine L Lawson; Andriy Kryshtafovych; Paul D Adams; Pavel V Afonine; Matthew L Baker; Benjamin A Barad; Paul Bond; Tom Burnley; Renzhi Cao; Jianlin Cheng; Grzegorz Chojnowski; Kevin Cowtan; Ken A Dill; Frank DiMaio; Daniel P Farrell; James S Fraser; Mark A Herzik; Soon Wen Hoh; Jie Hou; Li-Wei Hung; Maxim Igaev; Agnel P Joseph; Daisuke Kihara; Dilip Kumar; Sumit Mittal; Bohdan Monastyrskyy; Mateusz Olek; Colin M Palmer; Ardan Patwardhan; Alberto Perez; Jonas Pfab; Grigore D Pintilie; Jane S Richardson; Peter B Rosenthal; Daipayan Sarkar; Luisa U Schäfer; Michael F Schmid; Gunnar F Schröder; Mrinal Shekhar; Dong Si; Abishek Singharoy; Genki Terashi; Thomas C Terwilliger; Andrea Vaiana; Liguo Wang; Zhe Wang; Stephanie A Wankowicz; Christopher J Williams; Martyn Winn; Tianqi Wu; Xiaodi Yu; Kaiming Zhang; Helen M Berman; Wah Chiu
Journal:  Nat Methods       Date:  2021-02-04       Impact factor: 28.547

6.  TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows.

Authors:  Tristan Cragnolini; Harpal Sahota; Agnel Praveen Joseph; Aaron Sweeney; Sony Malhotra; Daven Vasishtan; Maya Topf
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-01-01       Impact factor: 7.652

7.  Assessing the utility of CASP14 models for molecular replacement.

Authors:  Claudia Millán; Ronan M Keegan; Joana Pereira; Massimo D Sammito; Adam J Simpkin; Airlie J McCoy; Andrei N Lupas; Marcus D Hartmann; Daniel J Rigden; Randy J Read
Journal:  Proteins       Date:  2021-08-21

8.  Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination.

Authors:  Yu Yamamori; Kentaro Tomii
Journal:  Int J Mol Sci       Date:  2022-02-10       Impact factor: 5.923

9.  Assessment of protein-protein interfaces in cryo-EM derived assemblies.

Authors:  Sony Malhotra; Agnel Praveen Joseph; Jeyan Thiyagalingam; Maya Topf
Journal:  Nat Commun       Date:  2021-06-07       Impact factor: 14.919

10.  Atomic model validation using the CCP-EM software suite.

Authors:  Agnel Praveen Joseph; Mateusz Olek; Sony Malhotra; Peijun Zhang; Kevin Cowtan; Tom Burnley; Martyn D Winn
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-01-24       Impact factor: 5.699

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