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Nucleic Acids Research, 2003, Vol. 31, No. 13 3404-3405
© 2003 Oxford University Press

SSEP: secondary structural elements of proteins

V. Shanthi, P. Selvarani, Ch. Kiran Kumar, C. S. Mohire and K. Sekar*

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

*To whom correspondence should be addressed. Tel: +91 803601409; Fax: +91 803600683; Email: sekar{at}physics.iisc.ernet.in

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 ß-strand fragments of varying lengths. In addition, it also contains the information about 310-helix, ß- 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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J. E. Gewehr and R. Zimmer
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles
Bioinformatics, January 15, 2006; 22(2): 181 - 187.
[Abstract] [Full Text] [PDF]


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