2012
DOI: 10.1107/s0021889812001501
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Fragment Finder 2.0: a computing server to identify structurally similar fragments

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 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 … Show more

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Cited by 5 publications
(3 citation statements)
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“…Such a numbering scheme may be used in order to preserve the homology. The reference protein may be numbered sequentially starting with 1, then the homologous protein from another species aligned to it (Balamurugan et al, 2007;Kumar & Sekar, 2010;Nagarajan et al, 2012). If residues are not present in the homologous sequence, residue numbers may be skipped so that alignment can be preserved (Kumar et al, 2009;Balamurugan et al, 2005).…”
Section: Introductionmentioning
confidence: 99%
“…Such a numbering scheme may be used in order to preserve the homology. The reference protein may be numbered sequentially starting with 1, then the homologous protein from another species aligned to it (Balamurugan et al, 2007;Kumar & Sekar, 2010;Nagarajan et al, 2012). If residues are not present in the homologous sequence, residue numbers may be skipped so that alignment can be preserved (Kumar et al, 2009;Balamurugan et al, 2005).…”
Section: Introductionmentioning
confidence: 99%
“…In X-ray crystallographic experiments, and thus in many of the three-dimensional structures deposited in the PDB, the loops and ends of the polypeptide chains and certain residues in the middle portion of the chain are not observed owing to poor electron density (Sumathi et al, 2006;Saravanan et al, 2010;Djinovic Carugo & Carugo, 2015;Gurusaran et al, 2016). Thus, these regions will not be available in the atomic coordinates file submitted to the PDB and they are referred to as 'missing regions' (Ananthalakshmi, Kumar et al, 2005;Ananthalakshmi, Samayamohan et al, 2005;Nagarajan et al, 2012;Santhosh et al, 2019). Depending on the location of the missing regions in a polypeptide chain, they can be classified into three categories: 'N-terminal' at the beginning of the polypeptide chain, 'C-terminal' at the end of the polypeptide chain, and 'Middle' anywhere between N-terminal and C-terminal.…”
Section: Introductionmentioning
confidence: 99%
“…Superimposé ( 5 ) combines several search algorithms such as TM-align ( 11 ) or CE ( 12 ) to search for fragments similar to a query. The FragFinder ( 6 ) search engine is based on the comparison of the main chain backbone conformational angles (ϕ and ψ). SA-Mot ( 7 ) is based on the encoding of structure as strings of a structural alphabet to search for over-represented conformations among collections of proteins with similar functions.…”
Section: Introductionmentioning
confidence: 99%