qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps

被引：29

作者：

Riley, Blake T. ^{[1
]}

Wankowicz, Stephanie A. ^{[2
,3
]}

de Oliveira, Saulo H. P. ^{[4
]}

van Zundert, Gydo C. P. ^{[5
]}

Hogan, Daniel W. ^{[2
]}

Fraser, James S. ^{[2
]}

Keedy, Daniel A. ^{[1
,6
,7
]}

van den Bedem, Henry ^{[2
,8
]}

机构：

[1] CUNY Adv Sci Res Ctr, Struct Biol Initiat, New York, NY 10031 USA

[2] Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94143 USA

[3] Univ Calif San Francisco, Biophys Grad Program, San Francisco, CA 94143 USA

[4] Frontier Med Corp, San Francisco, CA USA

[5] Schrodinger, New York, NY USA

[6] CUNY City Coll, Dept Chem & Biochem, New York, NY 10031 USA

[7] CUNY City Coll, Grad Ctr, PhD Programs Biochem Biol & Chem, New York, NY 10031 USA

[8] Atomwise Inc, San Francisco, CA 94103 USA

来源：

PROTEIN SCIENCE | 2021年 / 30卷 / 01期

基金：

美国国家科学基金会;

关键词：

conformational ensemble; cryo‐ electron microscopy; multiconformer models; protein dynamics; X‐ ray crystallography; SIDE-CHAIN; CONFORMATIONAL HETEROGENEITY; SERIAL SYNCHROTRON; ROOM-TEMPERATURE; OMIT MAPS; BINDING; REFINEMENT; ENSEMBLES;

D O I：

10.1002/pro.4001

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

New X-ray crystallography and cryo-electron microscopy (cryo-EM) approaches yield vast amounts of structural data from dynamic proteins and their complexes. Modeling the full conformational ensemble can provide important biological insights, but identifying and modeling an internally consistent set of alternate conformations remains a formidable challenge. qFit efficiently automates this process by generating a parsimonious multiconformer model. We refactored qFit from a distributed application into software that runs efficiently on a small server, desktop, or laptop. We describe the new qFit 3 software and provide some examples. qFit 3 is open-source under the MIT license, and is available at .

引用

页码：270 / 285

页数：16

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