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Nucleic Acids Research 2006 34(Web Server issue):W189-W193; doi:10.1093/nar/gkl205
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© 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

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels

J. Waldispühl1,2, Bonnie Berger2,3, Peter Clote1,4,* and Jean-Marc Steyaert5

1 Department of Biology, Boston College 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA 2 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, MA 02139, USA 3 Department of Mathematics, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge, Cambridge, MA 02139, USA 4 Department of Computer Science (courtesy appointment), Boston College 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA 5 Laboratoire d'Informatique (LIX), École Polytechnique 91128 Palaiseau, France

*To whom correspondence should be addressed. Tel: +1 617 552 1332; Fax: +1 617 552 2011; Email: clote{at}bc.edu

*Correspondence may also be addressed to Bonnie Berger. Email: bab{at}mit.edu

Received February 14, 2006. Revised March 22, 2006. Accepted March 22, 2006.

Transmembrane ß-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts. The cellular location and functional diversity of ß-barrel outer membrane proteins makes them an important protein class. At the present time, very few non-homologous TMB structures have been determined by X-ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane (TM) proteins. The transFold web server uses pairwise inter-strand residue statistical potentials derived from globular (non-outer-membrane) proteins to predict the supersecondary structure of TMB. Unlike all previous approaches, transFold does not use machine learning methods such as hidden Markov models or neural networks; instead, transFold employs multi-tape S-attribute grammars to describe all potential conformations, and then applies dynamic programming to determine the global minimum energy supersecondary structure. The transFold web server not only predicts secondary structure and TMB topology, but is the only method which additionally predicts the side-chain orientation of transmembrane ß-strand residues, inter-strand residue contacts and TM ß-strand inclination with respect to the membrane. The program transFold currently outperforms all other methods for accuracy of ß-barrel structure prediction. Available at http://bioinformatics.bc.edu/clotelab/transFold.


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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]


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