ProteinDBS: a real-time retrieval system for protein structure comparison
Medical and Biological Digital Library Research Lab, 322 Engineering Building North and 1 Digital Biology Lab, 302 Engineering Building North, Department of Computer Science, University of Missouri, Columbia, MO 65211-2060, USA
* To whom correspondence should be addressed. Tel: +1 573 882 3842; Fax: +1 573 882 3813; Email: shyuc{at}missouri.edu
The authors wish it to be known that, in their opinion, all authors should be regarded as joint First Authors
Received February 15, 2004; Revised and Accepted April 15, 2004
We have developed a web server (ProteinDBS) for the life science community to search for similar protein tertiary structures in real time. This system applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains. When meaningful contents, represented in a multi-dimensional feature space, have been extracted from distance matrices, an advanced indexing structure, Entropy Balanced Statistical (EBS) k-d tree, is utilized to index the data. Our system is able to return search results in ranked order from a database with 46 075 chains in seconds, exhibiting a reasonably high degree of precision. To our knowledge, this is the first real-time search engine for protein structure comparison. ProteinDBS provides two types of query method: query by Protein Data Bank protein chain ID and by new structures uploaded by users. The system is hosted at http://ProteinDBS.rnet.missouri.edu.
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