Recognition of binding patterns common to a set of protein structures

Maxim Shatsky*, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson

*Corresponding author for this work

Research output: Contribution to journalConference articlepeer-review


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 k-partite 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 method guarantees detection of an approximate solution in terms of pattern proximity as well as cardinality of multiple alignment. We show applications of MultiBind to several biological targets. The method recognizes patterns which are responsible for binding small molecules such as estradiol, ATP/ANP and transition state analogues. The presented computational results agree with the available biological ones.

Original languageEnglish
Pages (from-to)440-455
Number of pages16
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
StatePublished - 2005
Event9th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2005 - Cambridge, MA, United States
Duration: 14 May 200518 May 2005


  • Consensus binding patterns
  • K-partite matching
  • Multiple structure alignment of binding sites
  • Pattern discovery, recognition of functional sites
  • Pattern matching


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