CE-MC: a multiple protein structure alignment server
1 San Diego Supercomputer Center and 2 Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA and 3 The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
* To whom correspondence should be addressed. Tel: +1 858 822 0895; Fax: +1 858 534 8303; Email: babu{at}sdsc.edu
Received February 13, 2004; Revised and Accepted April 28, 2004
CE-MC server (http://cemc.sdsc.edu) provides a web-based facility for the alignment of multiple protein structures based on C-
coordinate distances, using combinatorial extension (CE) and Monte Carlo (MC) optimization methods. Alignments are possible for user-selected PDB (Protein Data Bank) chains as well as for user-uploaded structures or the combination of the two. The whole process of generating multiple structure alignments involves three distinct steps, i.e. all-to-all pairwise alignment using the CE algorithm, iterative global optimization of a multiple alignment using the MC algorithm and formatting MC results using the JOY program. The server can be used to get multiple alignments for up to 25 protein structural chains with the flexibility of uploading multiple coordinate files and performing multiple structure alignment for user-selected PDB chains. For large-scale jobs and local installation of the CE-MC program, users can download the source code and precompiled binaries from the web server.
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 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.
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