Addressing the Docking Problem: Finding Similar 3-D Protein Envelopes for Computer-Aided Drug Design

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Proceedings titleAdvances in Computational Biology
Series titleAdvances in Experimental Medicine and Biology; Volume 680
ConferenceThe 2009 International Conference on Bioinformatics and Computational Biology, Las Vegas, Nevada, July 13-16, 2009
SubjectPattern classification and recognition; Proteomics; Protein folding
AbstractConsider a protein (PX) that has been identified, during drug design, to constitute a new breakthrough in the design of a drug for treating a terminal illness. That is, this protein has the ability to dock on active sites and mask the subsequent docking of harmful foreign proteins. Unfortunately, protein X has serious side-effects and is therefore not suitable for use in drug design. Suppose another protein (PY) with similar outer structure (or envelope) and functionality, but without these side-effects, exists. Locating, and using, such an alternative protein has obvious benefits. This paper introduces an approach to locate such similar protein envelopes by considering their three-dimensional (3-D) shapes. We present a system which indexes and searches a large 3-D protein database and illustrate its effectiveness against a very large protein repository.
Publication date
AffiliationNational Research Council Canada (NRC-CNRC); NRC Institute for Information Technology
Peer reviewedYes
NPARC number16435929
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Record identifier58b91905-7ccb-404b-acd4-6cdb2bd2b1dd
Record created2010-11-25
Record modified2016-05-09
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