ArtSurf: a method for deformable partial matching of protein small-molecule binding sites

Authors:
Jeffrey R. Van Voorst;Yiying Tong;Leslie A. Kuhn
Affiliations:
University of Minnesota--Twin, Cities;Michigan State University;Michigan State University
Venue:
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Year:
2012

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Abstract

Proteins and many other biologically relevant molecules are flexible, and the flexibility of a given molecule is one of its important characteristics. In particular, the degree of global and local flexibility of proteins is an important characteristic of protein small-molecule binding sites. In this article, the binding site comparison problem [31, 11, 20, 30, 24, 33] is presented as a deformable partial surface matching problem [7, 13]. The problem is labeled as partial matching because we seek the best match for a given smaller query site (e.g. a small molecule fragment binding site) with respect to each larger binding site (in the search dataset). The question we address is "how can a given part of a binding site be realistically deformed to obtain the best partial match between that part and a full binding site"? This goal is addressed by optimizing the similarity between the site representations subject to modeling the proteins as kinematic chains. The preliminary results of our implementation (ArtSurf) show that the proposed approach is feasible, and that the implementation gives physically reasonable results which improve the detection of partial binding site similarity.