Recognition of Binding Patterns Common to a Set of Protein Structures

We present a novel computational method, MultiBind, for recognition of binding patterns common to a set of protein structures. It is the first method which performs a multiple alignment between protein binding sites in the absence of overall sequence, fold or binding partner similarity. MultiBind recognizes common spatial arrangements of physico-chemical properties in the binding sites. These should be important for recognition of function, prediction of binding and drug design. We discuss the theoretical aspects of the computational problem of multiple structure alignment. This problem involves solving a 3D kpartite matching problem, which we show to be NP-Hard. The MultiBind method, applies an efficient Geometric Hashing technique to detect a potential set of multiple alignments of the given binding sites. To overcome the exponential number of possible multiple combinations it applies a very efficient filtering procedure which is heavily based on the selected scoring function. Our me...

• Type: Conference
• Year: 2005
• Where: RECOMB
• Authors: Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson
• Keywords: Binding Sites, Computational Biology, Geometric Hashing Technique, RECOMB 2005, Transition State Analogues