UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System
By Zheng Yang, Keren Lasker, Dina Schneidman-Duhovny, Ben M. Webb, Conrad C. Huang, Eric F. Pettersen, Thomas D. Goddard, Elaine C. Meng, Andrej Sali, T. Ferrin. 2011
626 citations recorded by the source corpus.
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, IMP 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.
Subfields: Materials Chemistry, Molecular Biology, Structural Biology
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In Materials Chemistry
- Ben M. Webb
- Andrej Sali
- Dina Schneidman-Duhovny
- Keren Lasker
- Jianlin Cheng
- Yang Zhang
- Min-Yi Shen
- Jinbo Xu
In Molecular Biology
- Ben M. Webb
- Andrej Sali
- Dina Schneidman-Duhovny
- Keren Lasker
- Jianlin Cheng
- Yang Zhang
- Torsten Schwede
- Min-Yi Shen
In Structural Biology
Citations in the corpus
- Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies (2012, methodology): “The resulting clusters and the constituent models as well as restraints can be exported to Chimera [24] and Pymol [25] for visual inspection and further analysis.”
- Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, neutral): “…http://modelarchive.org HHpred http://toolkit.tuebingen.mpg.de/hhpred (Hildebrand et al., 2009) IMP http://www.salilab.org/imp (Russel et al., 2012; Yang et al., 2012) IntFOLD http://www.reading.ac.uk/bioinf/IntFOLD/ (Roche et al., 2011) I-Tasser http://zhanglab.ccmb.med.umich.edu/I-TASSER/…”