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

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 residu

SUBMITTER: Rose A 

PROVIDER: S-EPMC2703963 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature