Predictions of Protein-Protein Interactions at the Atomic Scale

  • Shoshana J. Wodak
  • Raúl Mendez
  • Marc Lensink

The use of computational procedures to predict protein-protein interactions from sequence and structure information has attracted renewed interest in recent years with the realization that such procedures can fruitfully complement and guide experimental characterizations of these interactions. CAPRI (Critical Assessment of Predicted Interactions) the community-wide experiment for assessing blind predictions of protein complexes is playing an important role in fostering progress in protein docking algorithms – the computational procedures for predicting the 3D structure of a protein complex from those of the individual components. In this paper we provide our view of the major challenges that docking algorithms must meet. We then describe how current docking methods address these challenges by presenting a summary of results obtained in rounds 1-5 of the CAPRI experiment, and discuss the lessons learned from these results.

Keywords: protein interactions, protein complexes, docking, structure, predictions, homology modeling, side chain optimization, energy, calculations, conformational sampling

Keywords

Hydration Shale Trypsin Lactobacillus Saccharomyces 

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Copyright information

© Springer 2007

Authors and Affiliations

  • Shoshana J. Wodak
    • 1
  • Raúl Mendez
    • 2
  • Marc Lensink
    • 2
  1. 1.Structural Biology ProgramHospital for Sick ChildrenCanada
  2. 2.Service de Conformation de Macromolécules Biologiques, et BioinformatiqueCentre de Biologie Structurale et BioinformatiqueBelgium

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