Segmenting motifs in protein-protein interface surfaces

  • Authors:
  • Jeff M. Phillips;Johannes Rudolph;Pankaj K. Agarwal

  • Affiliations:
  • Department of Computer Science, Duke University;Department of Biochemistry, Duke University;Department of Computer Science, Duke University

  • Venue:
  • WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
  • Year:
  • 2006

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Abstract

Protein-protein interactions form the basis for many intercellular events. In this paper we develop a tool for understanding the structure of these interactions. Specifically, we define a method for identifying a set of structural motifs on protein-protein interface surfaces. These motifs are secondary structures, akin to α-helices and β-sheets in protein structure; they describe how multiple residues form knob-into-hole features across the interface. These motifs are generated entirely from geometric properties and are easily annotated with additional biological data. We point to the use of these motifs in analyzing hotspot residues.