UCSF ChimeraX: Tools for structure building and analysis

Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at challenging resolutions of 3–4 Å. We describe new methods in the UCSF ChimeraX molecular modeling package that take advantage of machine‐learni...

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Bibliographic Details
Published inProtein science Vol. 32; no. 11; pp. e4792 - n/a
Main Authors Meng, Elaine C., Goddard, Thomas D., Pettersen, Eric F., Couch, Greg S., Pearson, Zach J., Morris, John H., Ferrin, Thomas E.
Format Journal Article
LanguageEnglish
Published Hoboken, USA John Wiley & Sons, Inc 01.11.2023
Wiley Subscription Services, Inc
Subjects
AlphaFold
atomic model building
ChimeraX
Cryoelectron Microscopy - methods
cryo‐electron microscopy
Electron microscopy
Likelihood Functions
Machine learning
Microscopy, Electron
Modelling
Models, Molecular
Molecular modelling
Protein Conformation
protein structure prediction
refinement
Software
Tools for Protein Science
refinement
atomic model building
protein structure prediction
AlphaFold
ChimeraX
cryo-electron microscopy
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Summary:Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at challenging resolutions of 3–4 Å. We describe new methods in the UCSF ChimeraX molecular modeling package that take advantage of machine‐learning structure predictions, provide likelihood‐based fitting in maps, and compute per‐residue scores to identify modeling errors. Additional model‐building tools assist analysis of mutations, post‐translational modifications, and interactions with ligands. We present the latest ChimeraX model‐building capabilities, including several community‐developed extensions. ChimeraX is available free of charge for noncommercial use at https://www.rbvi.ucsf.edu/chimerax.
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Review Editor: Nir Ben‐Tal
ISSN:0961-8368
1469-896X
1469-896X
DOI:10.1002/pro.4792