Nucleic Acids Research Advance Access published online on May 22, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp418
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Web Server Issue |
RHYTHM—a server to predict the orientation of transmembrane helices in channels and membrane-coils
1Institute for Medical Physics and Biophysics, Charité, University Medicine Berlin, Ziegelstrasse 5-9, 10098 Berlin, 2Institute for Theoretical Biology, Humboldt University, Invalidenstraße 43, 10115 Berlin, 3Institute for Biochemistry, Charité, University Medicine Berlin, Monbijoustrasse 2, 10117 Berlin and 4Institute of Physiology, Charité, University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany
*To whom correspondence should be addressed. Tel: +49 30 450 524 155; Fax: +49 30 450 524 952; Email: peter.hildebrand{at}charite.de
Received February 22, 2009. Revised April 18, 2009. Accepted May 6, 2009.
RHYTHM is a web server that predicts buried versus exposed residues of helical membrane proteins. Starting from a given protein sequence, secondary and tertiary structure information is calculated by RHYTHM within only a few seconds. The prediction applies structural information from a growing data base of precalculated packing files and evolutionary information from sequence patterns conserved in a representative dataset of membrane proteins (‘Pfam-domains’). The program uses two types of position specific matrices to account for the different geometries of packing in channels and transporters (‘channels’) or other membrane proteins (‘membrane-coils’). The output provides information on the secondary structure and topology of the protein and specifically on the contact type of each residue and its conservation. This information can be downloaded as a graphical file for illustration, a text file for analysis and statistics and a PyMOL file for modeling purposes. The server can be freely accessed at: URL: http://proteinformatics.de/rhythm