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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp963
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder

Michail Yu. Lobanov1, Benjamin A. Shoemaker2, Sergiy O. Garbuzynskiy1, Jessica H. Fong2, Anna R. Panchenko2 and Oxana V. Galzitskaya1,*

1Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia and 2National Center for Biotechnology Information, NIH, Bethesda, MD, USA

*To whom correspondence should be addressed. Tel/Fax: +7-495-6327871; Email: ogalzit{at}vega.protres.ru

Received August 14, 2009. Revised October 9, 2009. Accepted October 13, 2009.

Most of the proteins in a cell assemble into complexes to carry out their function. In this work, we have created a new database (named ComSin) of protein structures in bound (complex) and unbound (single) states to provide a researcher with exhaustive information on structures of the same or homologous proteins in bound and unbound states. From the complete Protein Data Bank (PDB), we selected 24 910 pairs of protein structures in bound and unbound states, and identified regions of intrinsic disorder. For 2448 pairs, the proteins in bound and unbound states are identical, while 7129 pairs have sequence identity 90% or larger. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes. Besides that, through our web server, one can obtain necessary information for studying disorder-to-order and order-to-disorder transitions upon complex formation, and analyze structural differences between proteins in bound and unbound states. The database is available at http://antares.protres.ru/comsin/.


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