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Biophys J. 2015 May 5;108(9):2097-102. doi: 10.1016/j.bpj.2015.03.051.

Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins.

Author information

1
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California; Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, San Francisco, California.
2
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California; Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, San Francisco, California; California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California.
3
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California; Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, San Francisco, California; California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California. Electronic address: tef@cgl.ucsf.edu.

Abstract

Homology modeling predicts protein structures using known structures of related proteins as templates. We developed MULTIDOMAIN ASSEMBLER (MDA) to address the special problems that arise when modeling proteins with large numbers of domains, such as fibronectin with 30 domains, as well as cases with hundreds of templates. These problems include how to spatially arrange nonoverlapping template structures, and how to get the best template coverage when some sequence regions have hundreds of available structures while other regions have a few distant homologs. MDA automates the tasks of template searching, visualization, and selection followed by multidomain model generation, and is part of the widely used molecular graphics package UCSF CHIMERA (University of California, San Francisco). We demonstrate applications and discuss MDA's benefits and limitations.

PMID:
25954868
PMCID:
PMC4423039
DOI:
10.1016/j.bpj.2015.03.051
[Indexed for MEDLINE]
Free PMC Article

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