Literature DB >> 33404524

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

Tristan Cragnolini1, Harpal Sahota1, Agnel Praveen Joseph1, Aaron Sweeney1, Sony Malhotra1, Daven Vasishtan2, Maya Topf1.   

Abstract

Structural determination of molecular complexes by cryo-EM requires large, often complex processing of the image data that are initially obtained. Here, TEMPy2, an update of the TEMPy package to process, optimize and assess cryo-EM maps and the structures fitted to them, is described. New optimization routines, comprehensive automated checks and workflows to perform these tasks are described. open access.

Entities:  

Keywords:  TEMPy2; fitting scores; macromolecular complexes; model assessment; model fitting; three-dimensional electron microscopy; validation

Mesh：

Substances：

Year:  2021        PMID： 33404524      PMCID： PMC7787107          DOI： 10.1107/S2059798320014928

Source DB:  PubMed          Journal:  Acta Crystallogr D Struct Biol        ISSN： 2059-7983            Impact factor:   7.652


  28 in total

1.  Scoring functions for cryoEM density fitting.

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

2.  Cryo-EM model validation using independent map reconstructions.

Authors:  Frank DiMaio; Junjie Zhang; Wah Chiu; David Baker
Journal:  Protein Sci       Date:  2013-06       Impact factor: 6.725

3.  Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

Authors:  J M de la Rosa-Trevín; A Quintana; L Del Cano; A Zaldívar; I Foche; J Gutiérrez; J Gómez-Blanco; J Burguet-Castell; J Cuenca-Alba; V Abrishami; J Vargas; J Otón; G Sharov; J L Vilas; J Navas; P Conesa; M Kazemi; R Marabini; C O S Sorzano; J M Carazo
Journal:  J Struct Biol       Date:  2016-04-20       Impact factor: 2.867

4.  MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography.

Authors:  Anchi Cheng; Richard Henderson; David Mastronarde; Steven J Ludtke; Remco H M Schoenmakers; Judith Short; Roberto Marabini; Sargis Dallakyan; David Agard; Martyn Winn
Journal:  J Struct Biol       Date:  2015-04-13       Impact factor: 2.867

5.  Recent developments in the CCP-EM software suite.

Authors:  Tom Burnley; Colin M Palmer; Martyn Winn
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-05-31       Impact factor: 7.652

6.  TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits.

Authors:  Irene Farabella; Daven Vasishtan; Agnel Praveen Joseph; Arun Prasad Pandurangan; Harpal Sahota; Maya Topf
Journal:  J Appl Crystallogr       Date:  2015-06-27       Impact factor: 3.304

7.  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

8.  Structural basis of human kinesin-8 function and inhibition.

Authors:  Julia Locke; Agnel Praveen Joseph; Alejandro Peña; Martin M Möckel; Thomas U Mayer; Maya Topf; Carolyn A Moores
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-23       Impact factor: 11.205

9.  Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate.

Authors:  Dejian Zhou; Xing Zhu; Sanduo Zheng; Dan Tan; Meng-Qiu Dong; Keqiong Ye
Journal:  Protein Cell       Date:  2018-03-19       Impact factor: 14.870

10.  Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy.

Authors:  Alejandro Peña; Aaron Sweeney; Alexander D Cook; Julia Locke; Maya Topf; Carolyn A Moores
Journal:  Structure       Date:  2020-02-20       Impact factor: 5.871
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  6 in total

1.  Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly.

Authors:  Jiahua He; Peicong Lin; Ji Chen; Hong Cao; Sheng-You Huang
Journal:  Nat Commun       Date:  2022-07-13       Impact factor: 17.694

2.  Cryo-EM targets in CASP14.

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

3.  EMDA: A Python package for Electron Microscopy Data Analysis.

Authors:  Rangana Warshamanage; Keitaro Yamashita; Garib N Murshudov
Journal:  J Struct Biol       Date:  2021-12-13       Impact factor: 2.867

4.  Cryo-EM single-particle structure refinement and map calculation using Servalcat.

Authors:  Keitaro Yamashita; Colin M Palmer; Tom Burnley; Garib N Murshudov
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-09-29       Impact factor: 7.652

5.  Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM.

Authors:  Adam J Simpkin; Martyn D Winn; Daniel J Rigden; Ronan M Keegan
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-10-20       Impact factor: 7.652

6.  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
  6 in total

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