Bioinformatics Advance Access published online on May 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth326
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 School of Information and Computer Science, University of California, Irvine, CA 92697; Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697
* To whom correspondence should be addressed. E-mail: pfbaldi{at}ics.uci.edu.
Motivation: Interchain Results: We have created a comprehensive database of ICBS interactions that is updated on a weekly basis and allows entries to be sorted and searched by relevance and other criteria through a simple Web interface. We derive a simple ICBS index to quantify the relative contributions of the Availability: The database is available at: http://www.igb.uci.edu/servers/icbs/. Supplementary Information: http://www.igb.uci.edu/servers/icbs/.
Revised March 4, 2004
Accepted May 15, 2004
Article
ICBS: a database of interactions between protein chains mediated by
-sheet formation
2 School of Information and Computer Science, University of California, Irvine, CA 92697; Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697; IUP Génie Physiologique et Informatique, University of Poitiers, 86000 Poitiers, France
3 Department of Chemistry, University of California, Irvine, CA 92697; Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697
4 Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697; Department of Biological Chemistry, University of California, Irvine, CA 92697
Abstract 
-sheet (ICBS) interactions occur widely in protein quaternary structures, interactions between proteins, and protein aggregation. These interactions play a central role in many biological processes and in diseases ranging from AIDS and cancer to anthrax and Alzheimer's.-ladders in the overall interchain interaction and compute first- and second-order statistics regarding amino acid composition and pairing at different relative positions in the -strands. Analysis of the database reveals a 15.8% prevalence of significant ICBS interactions, the majority of which involve the formation of antiparallel -sheets and many of which involve the formation of dimers and oligomers. The frequencies of amino acids in ICBS interfaces are similar to those in intrachain -sheet interfaces. A full range of non-covalent interactions between side chains complement the hydrogen-bonding interactions between the main chains. Polar amino acids pair preferentially with polar amino acids and nonpolar amino acids pair preferentially with nonpolar amino acids among antiparallel (i, j) pairs. We anticipate that the statistics and insights gained from the database will guide the development of agents that control interchain -sheet interactions and that the database will help identify new protein interactions and targets for these agents.
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