Koczyk Grzegorz, Berezovsky Igor N
Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen 5008, Norway.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W239-45. doi: 10.1093/nar/gkn326. Epub 2008 May 23.
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.
