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Nucleic Acids Research 2005 33(Web Server Issue):W193-W197; doi:10.1093/nar/gki360
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© The Author 2005. 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{at}oupjournals.org

Article

Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations

Hongyi Zhou1, Chi Zhang1, Song Liu1 and Yaoqi Zhou1,2,*

1Department of Physiology & Biophysics, Howard Hughes Medical Institute Center for Single Molecule Biophysics, State University of New York at Buffalo 124 Sherman Hall, Buffalo, NY 14214, USA 2Department of Macromolecular Science, The Key Laboratory of Molecular Engineering of Polymers, Fudan University Shanghai, China

*To whom correspondence should be addressed at Department of Physiology & Biophysics, Howard Hughes Medical Institute Center for Single Molecule Biophysics, State University of New York at Buffalo, 124 Sherman Hall, Buffalo, NY 14214, USA. Tel: +1 716 829 2985; Fax: +1 716 829 2344; Email: yqzhou{at}buffalo.edu

Received January 17, 2005. Revised February 11, 2005. Accepted February 22, 2005.

We have developed the following web servers for protein structural modeling and analysis at http://theory.med.buffalo.edu: THUMBUP, UMDHMMTMHP and TUPS, predictors of transmembrane helical protein topology based on a mean-burial-propensity scale of amino acid residues (THUMBUP), hidden Markov model (UMDHMMTMHP) and their combinations (TUPS); SPARKS 2.0 and SP3, two profile–profile alignment methods, that match input query sequence(s) to structural templates by integrating sequence profile with knowledge-based structural score (SPARKS 2.0) and structure-derived profile (SP3); DFIRE, a knowledge-based potential for scoring free energy of monomers (DMONOMER), loop conformations (DLOOP), mutant stability (DMUTANT) and binding affinity of protein–protein/peptide/DNA complexes (DCOMPLEX & DDNA); TCD, a program for protein-folding rate and transition-state analysis of small globular proteins; and DOGMA, a web-server that allows comparative analysis of domain combinations between plant and other 55 organisms. These servers provide tools for prediction and/or analysis of proteins on the secondary structure, tertiary structure and interaction levels, respectively.


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