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. © 2010 Springer Science+Business Media, LLC.