A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

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Tuncbag N., Kar G., Keskin O., Gursoy A., NUSSINOV R.

BRIEFINGS IN BIOINFORMATICS, vol.10, no.3, pp.217-232, 2009 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Review
  • Volume: 10 Issue: 3
  • Publication Date: 2009
  • Doi Number: 10.1093/bib/bbp001
  • Journal Name: BRIEFINGS IN BIOINFORMATICS
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Page Numbers: pp.217-232
  • Keywords: protein-protein interactions, protein-protein interfaces, binding site prediction, docking, web servers, databases, BINDING SITE PREDICTION, HOT-SPOTS, SHAPE COMPLEMENTARITY, QUATERNARY STRUCTURE, DOMAIN-DOMAIN, DATABASE, RESIDUES, CONSERVATION, RECOGNITION, COMPLEXES
  • Middle East Technical University Affiliated: No

Abstract

The unanimous agreement that cellular processes are (largely) governed by interactions between proteins has led to enormous community efforts culminating in overwhelming information relating to these proteins; to the regulation of their interactions, to the way in which they interact and to the function which is determined by these interactions. These data have been organized in databases and servers. However, to make these really useful, it is essential not only to be aware of these, but in particular to have a working knowledge of which tools to use for a given problem; what are the tool advantages and drawbacks; and no less important how to combine these for a particular goal since usually it is not one tool, but some combination of tool-modules that is needed. This is the goal of this review.