SSEP: secondary structural elements of proteins

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/.

SSEP-2.0: Secondary Structural Elements of Proteins

“…Thus, analysis of a specific sequence or a structural motif is greatly enhanced by determining the sequence, structure and functional relationships between the individual proteins. To the best of the knowledge of the authors, there is no efficient computing server (including the earlier version of SSEP; Shanthi et al, 2003) to search for and superpose a particular secondary-structural element from the same or different nonredundant (25 and 90%) protein chains (Hobohm & Sander, 1994). In addition, there is no mechanism available to delineate different types ofand -turns available in the non-redundant protein chains.…”

“…The updated search engine addresses these issues in detail and offers several useful utilities (see x3 for details) for the user's convenience. Hence, in this paper we will present only the enhanced facilities (compared with the earlier version of SSEP; Shanthi et al, 2003) in detail.…”

Ion pairs in non-redundant protein structures

“…Of the observed ion pairs, the percentage of individual basic and acidic residues involved in ion pair formation was also calculated and these residues were classifi ed based on their geometrical orientations. The knowledgebase SSEP (Balamurugan et al 2005;Shanthi et al 2003) was deployed to get the secondary structural elements and the residues involved in ion pairs were analysed.…”

PSAP: protein structure analysis package

“…Furthermore, by using the option 'Side-chain conformation angles', users can visualize the side-chain conformation angles for a particular amino acid residue present in the protein structure (Sheik et al, 2003). The option 'Secondary structural elements' displays all secondary structural elements available in the chosen protein structure and finds the percentage of the same (Shanthi, Selvarani et al, 2003). Information such as displaying a helical wheel plot of a particular helix and search facilities to look for the occurrence of the same secondary structural sequence motif in various sequence databases, such as the genome sequence database, SWISS-PROT, PIR and PDB, are provided (Balamurugan et al, 2005).…”