Fragment Finder 2.0: a computing server to identify structurally similar fragments

Nagarajan, R and Balan, Siva S and Sabarinathan, R and Vaishnavi, Kirti M and Sekar, K (2012) Fragment Finder 2.0: a computing server to identify structurally similar fragments. In: Journal of Applied Crystallography, 45 (Part 2). pp. 332-334.

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Abstract

Fragment Finder 2.0 is a web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets. The computing server identifies structurally similar fragments using the protein backbone C alpha angles. In addition, the identified fragments can be superimposed using either of the two structural superposition programs, STAMP and PROFIT, provided in the server. The freely available Java plug-in Jmol has been interfaced with the server for the visualization of the query and superposed fragments. The server is the updated version of a previously developed search engine and employs an in-house-developed fast pattern matching algorithm. This server can be accessed freely over the World Wide Web through the URL http://cluster.physics.iisc.ernet.in/ff/.

Item Type:	Journal Article
Publication:	Journal of Applied Crystallography
Publisher:	International Union of Crystallography
Additional Information:	.
Keywords:	AMINO-ACID SEQUENCE;PROTEINS;REPEATS;DIVERGENCE;RESOLUTION; ALIGNMENT;DATABASE;MODEL;FIND
Department/Centre:	Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited:	14 Aug 2012 04:59
Last Modified:	14 Aug 2012 05:51
URI:	http://eprints.iisc.ac.in/id/eprint/44488

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