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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W575-80. doi: 10.1093/nar/gkp418. Epub 2009 May 22.

RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils.

Author information

1
Institute for Medical Physics and Biophysics, Charité, University Medicine Berlin, Ziegelstrasse 5-9, 10098 Berlin, Germany.

Abstract

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.

PMID:
19465378
PMCID:
PMC2703963
DOI:
10.1093/nar/gkp418
[Indexed for MEDLINE]
Free PMC Article

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