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Prism: Protein-Protein Interaction Prediction by Structural Matching

  • Ozlem Keskin
  • Ruth Nussinov
  • Attila Gursoy
Part of the Methods in Molecular Biology book series (MIMB, volume 484)

Abstract

Prism (protein interactions by structural matching) is a system that employs a novel prediction algorithm for protein-protein interactions. It adopts a bottom-up approach that combines structure and sequence conservation in protein interfaces. The algorithm seeks possible binary interactions between proteins through structure similarity and evolutionary conservation of known interfaces. It is composed of a database containing protein interface structures derived from the Protein Data Bank (PDB) and predicted protein-protein interactions. It also provides related information about the proteins and an interactive protein interface viewer. In the current version, 3799 structurally nonredundant interfaces are used to predict the interactions among 6170 proteins. A substantial number of interactions are verified in two publicly available interaction databases (DIP and BIND). As the verified interactions demonstrate the suitability of our approach, unverified ones may point to undiscovered interactions. Prism can be accessed through a user-friendly website (http://prism.ccbb.ku.edu.tr) and it will be updated regularly as new protein structures become available in the PDB. Users may browse through the nonredundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of structures similar to these interfaces, or see the results of interaction predictions for a particular protein. Another service provided is the interactive prediction. This is done by running the algorithm for the user input structures.

Key Words

Protein interactions protein interaction prediction protein interfaces protein databases 

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Copyright information

© Humana Press, Totowa, NJ 2008

Authors and Affiliations

  • Ozlem Keskin
    • 1
  • Ruth Nussinov
    • 2
    • 3
  • Attila Gursoy
    • 1
  1. 1.Center for Computational Biology and Bioinformatics and College of EngineeringKoc UniversityIstanbulTurkey
  2. 2.Basic Research ProgramSAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program NCI-FrederickFrederickUSA
  3. 3.Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of MedicineTel Aviv UniversityTel AvivIsrael

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