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

被引：23

作者：

Cragnolini, Tristan ^{[1
]}

Sahota, Harpal ^{[1
]}

Joseph, Agnel Praveen ^{[1
,5
]}

Sweeney, Aaron ^{[1
]}

Malhotra, Sony ^{[1
]}

Vasishtan, Daven ^{[2
]}

Topf, Maya ^{[1
,3
,4
]}

机构：

[1] Birkbeck Univ Coll London, Inst Struct & Mol Biol, London, England

[2] Univ Oxford, Oxford Particle Imaging Ctr, Wellcome Trust Ctr Human Genet, Div Struct Biol, Oxford, England

[3] Leibniz Inst Expt Virol, Heinrich Pette Inst, Ctr Struct Syst Biol, Hamburg, Germany

[4] Univ Klinikum Hamburg Eppendorf, Hamburg, Germany

[5] Res Complex Harwell, Sci & Technol Facil Council, Didcot, Oxon, England

来源：

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2021年 / 77卷

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会; 英国医学研究理事会;

关键词：

three-dimensional electron microscopy; model fitting; validation; fitting scores; model assessment; macromolecular complexes; TEMPy2; EM RECONSTRUCTIONS; RESOLUTION; MODEL; REFINEMENT; MAPS; FIT;

D O I：

10.1107/S2059798320014928

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：41 / 47

页数：7

共 50 条

[1] TEMPy: a Python']Python library for assessment of three-dimensional electron microscopy density fits
Farabella, Irene
Vasishtan, Daven
Joseph, Agnel Praveen
Pandurangan, Arun Prasad
Sahota, Harpal
Topf, Maya
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2015, 48 : 1314 - 1323
[2] pyPept: a python']python library to generate atomistic 2D and 3D representations of peptides
Ochoa, Rodrigo
Brown, J. B.
Fox, Thomas
JOURNAL OF CHEMINFORMATICS, 2023, 15 (01)
[3] UnBlocksgen: A Python']Python library for 3D rock mass generation and analysis
Rasmussen, Leandro Lima
SOFTWAREX, 2020, 12
[4] CityDPC: A Python']Python library for handling 3D city model datasets
Shamovich, Maxim
Raming, Simon
Malhotra, Avichal
van Treeck, Christoph
Frisch, Jerome
BAUPHYSIK, 2024, 46 (06) : 340 - 347
[5] Graph-based active learning of agglomeration (GALA): a Python']Python library to segment 2D and 3D neuroimages
Nunez-Iglesias, Juan
Kennedy, Ryan
Plaza, Stephen M.
Chakraborty, Anirban
Katz, William T.
FRONTIERS IN NEUROINFORMATICS, 2014, 8
[6] PlantGL: A Python']Python-based geometric library for 3D plant modelling at different scales
Pradal, C.
Boudon, F.
Nouguier, C.
Chopard, J.
Godin, C.
GRAPHICAL MODELS, 2009, 71 (1-6) : 1 - 21
[7] pyPept: a python library to generate atomistic 2D and 3D representations of peptides
Rodrigo Ochoa
J. B. Brown
Thomas Fox
Journal of Cheminformatics, 15
[8] Rigid-Body Fitting of Atomic Models on 3D Density Maps of Electron Microscopy
Kawabata, Takeshi
INTEGRATIVE STRUCTURAL BIOLOGY WITH HYBRID METHODS, 2018, 1105 : 219 - 235
[9] ReMo3D - an open-source Python']Python package for 2D and 3D simulation of normal and lateral resistivity logs
Wilkosz, Michal
GEOLOGY GEOPHYSICS AND ENVIRONMENT, 2022, 48 (02): : 195 - 211
[10] Im2mesh: A Python']Python Library to Reconstruct 3D Meshes from Scattered Data and 2D Segmentations, Application to Patient-Specific Neuroblastoma Tumour Image Sequences
Sainz-DeMena, Diego
Manuel Garcia-Aznar, Jose
Angeles Perez, Maria
Borau, Carlos
APPLIED SCIENCES-BASEL, 2022, 12 (22):

← 1 2 3 4 5 →