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Nucleic Acids Research 2005 33(Web Server Issue):W85-W88; doi:10.1093/nar/gki353
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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

Fragment Finder: a web-based software to identify similar three-dimensional structural motif

P. Ananthalakshmi1, Ch. Kiran Kumar1, M. Jeyasimhan1, K. Sumathi1 and K. Sekar1,2,*

1Bioinformatics Centre, Indian Institute of Science Bangalore 560 012, India 2Supercomputer Education and Research Centre, Indian Institute of Science Bangalore 560 012, India

*To whom correspondence should be addressed. Tel: +91 080 23601409/22923059; Fax: +91 080 23600085/23600551; Email: sekar{at}physics.iisc.ernet.in

Received November 19, 2004. Revised December 30, 2004. Accepted December 30, 2004.

FF (Fragment Finder) is a web-based interactive search engine developed to retrieve the user-desired similar 3D structural fragments from the selected subset of 25 or 90% non-homologous protein chains. The search is based on the comparison of the main chain backbone conformational angles ({varphi} and {phi}). Additionally, the queried motifs can be superimposed to find out how similar the structural fragments are, so that the information can be effectively used in molecular modeling. The engine has facilities to view the resultant superposed or individual 3D structure(s) on the client machine. The proposed web server is made freely accessible at the following URL: http://cluster.physics.iisc.ernet.in/ff/ or http://144.16.71.148/ff/.


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