UCSF Chimera, MODELLER, and IMP: An integrated modeling system

Zheng Yang, Keren Lasker, Dina Schneidman-Duhovny, Ben Webb, Conrad C. Huang, Eric F. Pettersen, Thomas D. Goddard, Elaine C. Meng, Andrej Sali*, Thomas E. Ferrin

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

464 Scopus citations

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.

Original languageAmerican English
Pages (from-to)269-278
Number of pages10
JournalJournal of Structural Biology
Volume179
Issue number3
DOIs
StatePublished - Sep 2012
Externally publishedYes

Bibliographical note

Funding Information:
The authors gratefully acknowledge Prof. Wah Chiu and Dr. Steven Ludtke for providing the SAXS experimental data for the GroEL example. The research of K. Lasker was supported by continuous mentorship from Prof. Haim J. Wolfson as well as a fellowship from the Clore Foundation Ph.D. Scholars program . K. Lasker’s research was carried out in partial fulfillment of the requirements for a Ph.D. degree from TAU. This work was funded by NIH Grants R01 GM083960 , U54 RR022220 , and PN2 EY016525 to A. Sali and P41 RR001081 to T.E. Ferrin.

Keywords

  • Electron microscopy
  • Integrative structural modeling
  • Interactive molecular visualization
  • Restraint-based modeling
  • Small-angle X-ray scattering

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