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. 2003 Jul 1;31(13):3404-5.
doi: 10.1093/nar/gkg507.

SSEP: Secondary structural elements of proteins

V Shanthi  1 , P Selvarani, Ch Kiran Kumar, C S Mohire, K Sekar
Affiliations

SSEP: Secondary structural elements of proteins

V Shanthi et al. Nucleic Acids Res. .

Abstract

SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein chains from 1670 protein structures and 6182 protein chains from 5425 protein structures in 25 and 90% non-redundant protein chains, respectively. The current version provides information about the alpha-helical segments and beta-strand fragments of varying lengths. In addition, it also contains the information about 3(10)-helix, beta- and nu-turns and hairpin loops. The free graphics program RASMOL has been interfaced with the search engine to visualize the three-dimensional structures of the user queried secondary structural fragment. The database is updated regularly and is available through Bioinformatics web server at http://cluster.physics.iisc.ernet.in/ssep/ or http://144.16.71.148/ssep/.

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Figures

Figure 1
Figure 1
The panel shows a sample output frame of a motif ‘QFNGM’ in all the secondary structural elements in 25% non-homologous protein structures. The motif is shown in ribbons while the remaining portion of the protein molecule is in the form of backbone trace.
See this image and copyright information in PMC

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References

    1. Bernstein F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F.,Jr, Brice,M.D., Rogers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M.J. (1977) The Protein Data Bank: a computer based archival file for macromolecular structures. J. Mol. Biol., 112, 535–542. - PubMed
    1. Islam S.A. and Sternberg,M.J.E. (1989) A relational database of protein structures designed for flexible enquiries about conformation. Protein Eng., 2, 431–442. - PubMed
    1. Guruprasad K., Prasad,M.S. and Kumar,G.R. (2000) Database of structural motifs in proteins. Bioinformatics, 16, 372–375. - PubMed
    1. Hobohm U. and Sander,C. (1994) Enlarged representative set protein structures. Protein Sci., 3, 522–524. - PMC - PubMed
    1. Hutchinson E.G. and Thornton,J.M. (1996) PROMOTIF—a program to identify and analyze secondary structural motifs in proteins. Protein Sci., 5, 212–220. - PMC - PubMed

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