Taking geometry to its edge: Fast unbound rigid (and hinge-bent) docking

Dina Schneidman-Duhovny, Yuval Inbar, Vladimir Polak, Maxim Shatsky, Inbal Halperin, Hadar Benyamini, Adi Barzilai, Oranit Dror, Nurit Haspel, Ruth Nussinov, Haim J. Wolfson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

We present a very efficient rigid "unbound" soft docking methodology, which is based on detection of geometric shape complementarity, allowing liberal steric clash at the interface. The method is based on local shape feature matching, avoiding the exhaustive search of the 6D transformation space. Our experiments at CAPRI rounds 1 and 2 show that although the method does not perform an exhaustive search of the 6D transformation space, the "correct" solution is never lost. However, such a solution might rank low for large proteins, because there are alternatives with significantly larger geometrically compatible interfaces. In many cases this problem can be resolved by successful a priori focusing on the vicinity of potential binding sites as well as the extension of the technique to flexible (hinge-bent) docking. This is demonstrated in the experiments performed as a lesson from our CAPRI experience.

Original languageEnglish
Pages (from-to)107-112
Number of pages6
JournalProteins: Structure, Function and Genetics
Volume52
Issue number1
DOIs
StatePublished - 1 Jul 2003

Keywords

  • Binding site focusing
  • CAPRI
  • Flexible docking
  • PatchDock
  • Unbound docking

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