UCSF Chimera, MODELLER, and IMP: An Integrated Modeling System

J Struct Biol. 2012 Sep;179(3):269-78. doi: 10.1016/j.jsb.2011.09.006. Epub 2011 Sep 22.

Abstract

Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several modeling tools into UCSF Chimera. These include comparative modeling by MODELLER, simultaneous fitting of multiple components into electron microscopy density maps by IMP MultiFit, computing of small-angle X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cattle
  • Computer Simulation*
  • Escherichia coli Proteins / chemistry
  • Heat-Shock Proteins / chemistry
  • Macromolecular Substances / chemistry
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Subunits / chemistry
  • Scattering, Small Angle
  • Software*
  • Structural Homology, Protein
  • X-Ray Diffraction

Substances

  • Escherichia coli Proteins
  • GroE protein, E coli
  • Heat-Shock Proteins
  • Macromolecular Substances
  • Protein Subunits