Skip Navigation

Nucleic Acids Research 2006 34(Web Server issue):W186-W188; doi:10.1093/nar/gkl262
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (496K) Freely available
Right arrow Screen PDF (380K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Bigelow, H.
Right arrow Articles by Rost, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bigelow, H.
Right arrow Articles by Rost, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins

Henry Bigelow1,2,* and Burkhard Rost1,2,3

1 CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University 630 West 168th Street, New York, NY 10032, USA 2 Columbia University Center for Computational Biology and Bioinformatics (C2B2) 1130 St. Nicholas Avenue Rm. 802, New York, NY 10032, USA 3 North East Structural Genomics Center (NESG), Irvine Cancer Center 1130 St. Nicholas Avenue Rm. 802, New York, NY 10032, USA

*To whom correspondence should be addressed. Tel: +1 212 851 4669; Fax: +1 212 851 5176; Email: hrbigelow{at}gmail.com

Received February 14, 2006. Revised March 1, 2006. Accepted March 31, 2006.

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% while whole-protein discrimination accuracy was 70 at 60% coverage. The PROFtmb web server includes all source code, training data and whole-proteome predictions from 78 Gram-negative bacterial genomes and is available freely and without registration at http://rostlab.org/services/proftmb.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
A. Randall, J. Cheng, M. Sweredoski, and P. Baldi
TMBpro: secondary structure, {beta}-contact and tertiary structure prediction of transmembrane {beta}-barrel proteins
Bioinformatics, February 15, 2008; 24(4): 513 - 520.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.