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Nucleic Acids Research 2005 33(Web Server Issue):W111-W115; doi:10.1093/nar/gki457
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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

AS2TS system for protein structure modeling and analysis

A. Zemla*, C. Ecale Zhou, T. Slezak, T. Kuczmarski, D. Rama, C. Torres, D. Sawicka and D. Barsky

Lawrence Livermore National Laboratory 7000 East Avenue, Livermore, CA 94550, USA

*To whom correspondence should be addressed at Computing Applications and Research, Energy, Environment, and Biology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA. Tel: +1 925 423 5571; Fax: +1 925 423 6437; Email: adamz{at}llnl.gov

Received February 15, 2005. Revised April 4, 2005. Accepted April 4, 2005.

We present a set of programs and a website designed to facilitate protein structure comparison and protein structure modeling efforts. Our protein structure analysis and comparison services use the LGA (local-global alignment) program to search for regions of local similarity and to evaluate the level of structural similarity between compared protein structures. To facilitate the homology-based protein structure modeling process, our AL2TS service translates given sequence–structure alignment data into the standard Protein Data Bank (PDB) atom records (coordinates). For a given sequence of amino acids, the AS2TS (amino acid sequence to tertiary structure) system calculates (e.g. using PSI-BLAST PDB analysis) a list of the closest proteins from the PDB, and then a set of draft 3D models is automatically created. Web services are available at http://as2ts.llnl.gov/.


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