Prediction of Protein‐Protein Interaction Networks

Shawn M. Gomez1, Kwangbom Choi2, Yang Wu1

1 Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 2 Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.2
DOI:  10.1002/0471250953.bi0802s22
Online Posting Date:  June, 2008
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Abstract

This unit offers a general overview of several techniques that have been developed for inferring functional and/or protein‐protein interaction networks. The majority of these use whole‐genome sequences as their primary input source of data. In addition, a few methods that utilize both protein features and experimental protein‐protein interaction data directly in the prediction of new interactions have recently been developed. While an exhaustive list of approaches is not presented, it is hoped that the reader will gain a sense of how these approaches are implemented and an idea of their relative strengths and weaknesses, and a broader perspective on the type of work being conducted in this highly active area of research. Curr. Protoc. Bioinform. 22:8.2.1–8.2.14. © 2008 by John Wiley & Sons, Inc.

Keywords: protein interactions; bioinformatics; interaction networks

     
 
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Table of Contents

  • Introduction
  • Approaches
  • Observations and Conclusions
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

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Internet Resources
   http://dip.doe‐mbi.ucla.edu
  The Database of Interacting Proteins (DIP). A database of both manually and automatically curated experimental protein‐protein interactions.
   http://string.embl.de
  STRING is a database of known and predicted protein‐protein interactions. The interactions include direct (physical) and indirect (functional) associations taken from high‐throughput experiments, genomic context, coexpression, and literature.
   http://www.bind.ca
  The Biomolecular Interaction Network Database (BIND). Database of interactions, molecular complexes, and pathways. Includes interactions other than protein‐protein (e.g., protein‐DNA).
   http://cbm.bio.uniroma2.it/mint
  The Molecular Interactions Database (MINT). A manually curated database designed to store functional interactions between biological molecules (i.e., proteins RNA and DNA).
   http://portal.curagen.com/extpc/com.curagen.portal.servlet.Yeast
  PathCalling Yeast Interaction Database. Database of results from Uetz et al. ().
   http://wit.mcs.anl.gov/WIT2
  The WIT homepage. A Web site of reconstructed metabolic pathways for a number of genomes.
   http://mips.gsf.de
  The Munich Information Center for Protein Sequences (MIPS) homepage. Maintains curated database designed to store functional interactions between biological molecules (e.g., proteins, RNA, DNA).
   http://www.genome.ad.jp/kegg
  KEGG: Kyoto Encyclopedia of Genes and Genomes. In addition to other material, this site provides a database of molecular interactions as well as metabolic and signal transduction pathways.
   http://www.ecocyc.org
  The Encyclopedia of Escherichia coli Genes and Metabolism (EcoCyc) Web site.
   http://pim.hybrigenics.com
  Web site for Hybrigenics’ Protein Interaction Map (PIM) functional proteomics software platform.
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