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Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks

  • Lisa Bartoli
  • Pier Luigi Martelli
  • Ivan Rossi
  • Piero Fariselli
  • Rita Casadio
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5688)

Abstract

Most of the cellular functions are the result of the concerted action of protein complexes forming pathways and networks. For this reason, efforts were devoted to the study of protein-protein interactions. Large-scale experiments on whole genomes allowed the identification of interacting protein pairs. However residues involved in the interaction are generally not known and the majority of the interactions still lack a structural characterization. A crucial step towards the deciphering of the interaction mechanism of proteins is the recognition of their interacting surfaces, particularly in those structures for which also the most recent interaction network resources do not contain information. To this purpose, we developed a neural network-based method that is able to characterize protein complexes, by predicting amino acid residues that mediate the interactions. All the Protein Data Bank (PDB) chains, both in the unbound and in the complexed form, are predicted and the results are stored in a database of interaction surfaces (http://gpcr.biocomp.unibo.it/zenpatches). Finally, we performed a survey on the different computational methods for protein-protein interaction prediction and on their training/testing sets in order to highlight the most informative properties of protein interfaces.

Keywords

protein-protein interaction site neural network patch smoothing interacting surfaces 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Lisa Bartoli
    • 1
  • Pier Luigi Martelli
    • 1
  • Ivan Rossi
    • 2
  • Piero Fariselli
    • 1
  • Rita Casadio
    • 1
  1. 1.CIRB/Department of BiologyBiocomputing Group, University of BolognaBolognaItaly
  2. 2.BioDec s.r.l., Casalecchio di RenoBolognaItaly

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