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Nucleic Acids Research Advance Access originally published online on May 23, 2008
Nucleic Acids Research 2008 36(Web Server issue):W239-W245; doi:10.1093/nar/gkn326
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W239-W245
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure

Grzegorz Koczyk1,2 and Igor N. Berezovsky1,*

1Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen 5008, Norway and 2Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland

*To whom correspondence should be addressed. Tel: +47 55 58 47 12; Fax: +47 55 58 42 95; Email: igor.berezovsky{at}bccs.uib.no

Received February 11, 2008. Revised April 24, 2008. Accepted May 7, 2008.

Domain hierarchy and closed loops (DHcL) (http://sitron.bccs.uib.no/dhcl/) is a web server that delineates energy hierarchy of protein domain structure and detects domains at different levels of this hierarchy. The server also identifies closed loops and van der Waals locks, which constitute a structural basis for the protein domain hierarchy. The DHcL can be a useful tool for an express analysis of protein structures and their alternative domain decompositions. The user submits a PDB identifier(s) or uploads a 3D protein structure in a PDB format. The results of the analysis are the location of domains at different levels of hierarchy, closed loops, van der Waals locks and their interactive visualization. The server maintains a regularly updated database of domains, closed loop and van der Waals locks for all X-ray structures in PDB. DHcL server is available at: http://sitron.bccs.uib.no/dhcl.


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