Fragment Finder 2.0: a computing server to identify structurally similar fragments
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 Cα angles. In addition, the identifie...
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| Veröffentlicht in: | Journal of applied crystallography 2012-04, Vol.45 (2), p.332-334 |
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| container_issue | 2 |
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| container_title | Journal of applied crystallography |
| container_volume | 45 |
| creator | Nagarajan, R. Siva Balan, S. Sabarinathan, R. Kirti Vaishnavi, M. Sekar, K. |
| description | 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 Cα 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/. |
| doi_str_mv | 10.1107/S0021889812001501 |
| format | Article |
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Appl. Cryst</addtitle><date>2012-04</date><risdate>2012</risdate><volume>45</volume><issue>2</issue><spage>332</spage><epage>334</epage><pages>332-334</pages><issn>1600-5767</issn><issn>0021-8898</issn><eissn>1600-5767</eissn><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 Cα 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. 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| ispartof | Journal of applied crystallography, 2012-04, Vol.45 (2), p.332-334 |
| issn | 1600-5767 0021-8898 1600-5767 |
| language | eng |
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| source | Wiley Online Library All Journals; Alma/SFX Local Collection |
| subjects | Algorithms Computation computer programs Crystallography Fragment Finder 2.0 Fragmentation Interactive Interactive computer systems Java (programming language) protein fragment identification Proteins Search engines Servers World Wide Web |
| title | Fragment Finder 2.0: a computing server to identify structurally similar fragments |
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