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Briefings in Bioinformatics Advance Access originally published online on February 24, 2009
Briefings in Bioinformatics 2009 10(3):217-232; doi:10.1093/bib/bbp001
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Nurcan Tuncbag, Gozde Kar, Ozlem Keskin, Attila Gursoy and Ruth Nussinov

Corresponding author. Ruth Nussinov, Center for Cancer Research Nanobiology Program, Bldg 469, Rm 151, SAIC, NCI-Frederick, Frederick. MD 21702 USA and Department of Human Genetics, Medical School, Tel Aviv University, Tel Aviv, Israel, 69978. Tel: 301-846-5579; Fax: 301-846-5598; E-mail: ruthnu{at}helix.nih.gov

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.

Keywords: protein–protein interactions, protein–protein interfaces, binding site prediction, docking, web servers, databases

Submitted: October 28, 2008. Received (in revised form): January 5, 2009.


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