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

ABSTRACT: 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 https://github.com/ExcitedStates/qfit-3.0.

SUBMITTER: Riley BT

PROVIDER: S-EPMC7737783 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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

Riley Blake T BT Wankowicz Stephanie A SA de Oliveira Saulo H P SHP van Zundert Gydo C P GCP Hogan Daniel W DW Fraser James S JS Keedy Daniel A DA van den Bedem Henry H

Protein science : a publication of the Protein Society 20201130 1

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 ...[more]

PMID: 33210433

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