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

doi:10.1016/j.jsb.2011.09.006

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 journal › Article › peer-review

482 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 language	English
Pages (from-to)	269-278
Number of pages	10
Journal	Journal of Structural Biology
Volume	179
Issue number	3
DOIs	https://doi.org/10.1016/j.jsb.2011.09.006
State	Published - Sep 2012
Externally published	Yes

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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10.1016/j.jsb.2011.09.006

Cite this

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title = "UCSF Chimera, MODELLER, and IMP: An integrated modeling system",

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.",

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author = "Zheng Yang and Keren Lasker and Dina Schneidman-Duhovny and Ben Webb and Huang, {Conrad C.} and Pettersen, {Eric F.} and Goddard, {Thomas D.} and Meng, {Elaine C.} and Andrej Sali and Ferrin, {Thomas E.}",

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{\textquoteright}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. ",

year = "2012",

month = sep,

doi = "10.1016/j.jsb.2011.09.006",

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AU - Pettersen, Eric F.

AU - Goddard, Thomas D.

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AU - Sali, Andrej

AU - Ferrin, Thomas E.

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KW - Restraint-based modeling

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

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Bibliographical note

Keywords

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