Segmenting Motifs in Protein-Protein Interface Surfaces

  • Jeff M. Phillips
  • Johannes Rudolph
  • Pankaj K. Agarwal
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)


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.


Interface Surface Interior Vertex Protein Interface Large Motif Watershed Algorithm 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Jeff M. Phillips
    • 1
  • Johannes Rudolph
    • 2
  • Pankaj K. Agarwal
    • 1
  1. 1.Department of Computer ScienceDuke University 
  2. 2.Department of BiochemistryDuke University 

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