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Bioinformatics Advance Access first published online on August 20, 2007
This version published online on August 21, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm356
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Con-Struct Map: a Comparative Contact Map Analysis Tool

Jo-Lan Chung 1,2,3, John E Beaver 3, Eric D Scheeff 3,4 and Philip E Bourne 2,3,*

1Department of Chemistry and Biochemistry, 2Skaggs School of Pharmacy and Pharmaceutical Sciences, 3San Diego Supercomputer Center, University of California, San Diego, Gilman Drive, La Jolla, CA 92093, USA. 4Present address: Razavi-Newman Center for Bioinformatics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd., La Jolla, CA 92037, USA

*To whom correspondence should be addressed. Philip E. Bourne, E-mail: pbourne{at}ucsd.edu


  Abstract

Summary: Con-Struct Map is a graphical tool for the comparative study of protein structures. The tool detects potential conserved residue contacts shared by multiple protein structures by superimposing their contact maps according to a multiple structure alignment. In general, Con-Struct Map allows the study of structural changes resulting from, for example, sequence substitutions, or alternatively, the study of conserved components of a structure framework across structurally aligned proteins. Specific applications include the study of sequence-structure relationship in distantly related proteins and the comparisons of wild type and mutated proteins.

Availability: http://pdbrs3.sdsc.edu/ConStructMap/viewer_argument_generator/singleArguments

Contact: pbourne{at}ucsd.edu

Associate Editor: Prof. Alsonso Valencia

Received on May 11, 2007; revised on July 1, 2007; accepted on July 3, 2007

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PConPy--a Python module for generating 2D protein maps
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[Abstract] [Full Text] [PDF]


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