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

Protein Sci. 2021 Jan;30(1):270-285. doi: 10.1002/pro.4001. Epub 2020 Nov 30.


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.

Keywords: X-ray crystallography; conformational ensemble; cryo-electron microscopy; multiconformer models; protein dynamics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Ligands
  • Models, Molecular*
  • Proteins / chemistry*
  • Software*


  • Ligands
  • Proteins