- Article -
| In Silico Biology 6, 0029 (2006); ©2006, Bioinformation Systems e.V. |
SSToSS - Sequence-Structural Templates of Single-member Superfamilies
Saikat Chakrabarti1,3, Gowri Manohari2, Ganesan Pugalenthi1 and Ramanathan Sowdhamini1*
1 National Centre for Biological Sciences, UAS-GKVK campus, Bellary Road, Bangalore 560 065, India
2 Avinashalingam Institute, Coimbatore 641 043, India
3 current address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
* Corresponding author
Email: mini@ncbs.res.in
Edited by E. Wingender; received April 01, 2006; revised and accepted May 27, 2006; published June 08, 2006
Abstract
The presence of sequence homologues and the availability of structural information of proteins enable better understanding of the biological function of a protein family. A majority of entries in protein structural databank are single member superfamilies for which it is hard to derive motifs due to the paucity of structural homologues. Important conserved segments for these superfamilies have been identified and compiled into a database, SSToSS (Sequence Structural Templates of Single member Superfamily). Conserved regions, recognized by permitted amino acid exchanges, are mapped on the structure and various structural features (solvent accessibility, secondary structure content, hydrogen bonding and residue packing) are examined. These conserved segments with high structural feature content are projected as sequence-structural templates for the particular superfamily member. Interactive three-dimensional displays of the templates in three-dimensional structure (in Chime® and RASMOL) are provided for better understanding and visualization. In SSToSS database, we also provide the application of sequence-structural templates in three different areas: multiple-motif based sequence search, multiple sequence alignment and homology modeling. In each case, the inclusion of the sequence-structural templates can give rise to sensitive and accurate results. This enables the inclusion of singletons to provide added value to the recognition of additional members, comparative modeling and in designing experiments.
Keywords: conserved regions, motif-based database search, comparative modeling, spatial orientation of motifs, superfamily signatures, distant similarity, protein structure prediction