Methods for Comparing Protein Surfaces and their Application to Binding Site Recognition
Discovery of a similar region on two protein surfaces can lead to important inference about the functional role
or molecular interaction of this region for one of the proteins if such information is available for the other.
This tutorial will present the basic principles of protein-protein interactions and review recent approaches to
compare protein surfaces and to recognize binding sites. It will focus on the geometric aspects of the protein
surface comparison problem. Topics covered include local shape descriptors for the representations of the
surfaces; basic data structures for modelling proteins; similarity measures; motif finding for the functional
annotation of proteins; application of methods developed in the area of computer vision to problems in protein
structure comparison.
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Bock ME, Garutti C, Guerra C. (2007). Effective Labelling of Molecular Surface Points to Matching Cavities and Locate Putative Binding Sites. Proc. Computational Systems Bioinformatics CSB , San Diego , 263-275.
Shulman-Peleg A, Nussinov R, Wolfson H.J. (2004). Recognition of Functional Sites in Protein Structures. J. Mol. Biol ., 339 , 607-633.