CE-MC: a multiple protein structure alignment server
CE-MC server (http://cemc.sdsc.edu) provides a web-based facility for the alignment of multiple protein structures based on C-α coordinate distances, using combinatorial extension (CE) and Monte Carlo (MC) optimization methods. Alignments are possible for user-selected PDB (Protein Data Bank) chains...
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| Published in: | Nucleic acids research Vol. 32; no. suppl-2; pp. W100 - W103 |
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| Main Authors: | , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
England
Oxford University Press
01-07-2004
Oxford Publishing Limited (England) |
| Subjects: | |
| Online Access: | Get full text |
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| Summary: | CE-MC server (http://cemc.sdsc.edu) provides a web-based facility for the alignment of multiple protein structures based on C-α 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. |
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| Bibliography: | To whom correspondence should be addressed. Tel: +1 858 822 0895; Fax: +1 858 534 8303; Email: babu@sdsc.edu istex:AB888B6EB0DAA585323E3B19A8F3F03F705EC31F local:gkh464 Received February 13, 2004; Revised and Accepted April 28, 2004 ark:/67375/HXZ-ZMGKCNW0-K ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 2004, the authors 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. |
| ISSN: | 0305-1048 1362-4962 |
| DOI: | 10.1093/nar/gkh464 |