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PROFtmb

swMATH ID: 11343
Software Authors: Bigelow, H.; Rost, B.
Description: PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. For each query protein, PROFtmb provides both a Z-value indicating that the protein actually contains a membrane barrel, and a four-state per-residue labeling of upward- and downward-facing strands, periplasmic hairpins and extracellular loops. While most users submit individual proteins known to contain TMBs, some groups submit entire proteomes to screen for potential TMBs. Response time is about 4 min for a 500-residue protein. PROFtmb is a profile-based Hidden Markov Model (HMM) with an architecture mirroring the structure of TMBs. The per-residue accuracy on the 8-fold cross-validated testing set is 86
Homepage: http://nar.oxfordjournals.org/content/34/suppl_2/W186.short
Related Software: BLAST; PSI-BLAST; TMB-Hunt; BOMP; Psortb; PRED-TMBB; LOCSVMPSI
Cited in: 2 Documents

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