title: Addressing the docking problem: finding similar 3-D protein envelopes for computer-aided drug design.
abstract: Consider a protein (P(X)) 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 (P(Y)) 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 (3D) shapes. We present a system which indexes and searches a large 3D protein database and illustrate its effectiveness against a very large protein repository.
authors.affiliation: Visual Information Technology, National Research Council, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada. eric.paquet@nrc-cnrc.gc.ca
authors.forename: Eric
authors.initials: E
authors.lastname: Paquet
authors.forename: Herna L
authors.initials: HL
authors.lastname: Viktor
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D003198:Computer Simulation; D017076:Computer-Aided Design / Q000706:statistics & numerical data*; D030562:Databases, Protein; D015195:Drug Design; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D040901:Proteomics
chemical_list: D011506:Proteins