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SSToSS - Sequence-Structural Templates of Single-member Superfamilies


NAR Molecular Biology Database Collection entry number 530
Chakrabarti, S.1, Manohari, G.2 and R. Sowdhamini1
1National Centre for Biological Sciences, UAS-GKVK campus, Bellary Road, Bangalore 560 065, INDIA
2Avinashalingam Institute, Coimbatore 641 043, INDIA

Database Description

Structurally conserved regions for 613 single member superfamilies of proteins are identified and compiled into a database, SSToSS (Sequence Structural Templates of Single member Superfamily). Information about the single member superfamilies are derived from PASS2 superfamily alignment database that is in direct correspondence with SCOP. This database can be viewed as an additional feature to the mainstream database of PASS2 (Mallika et al., 2002) for every single member superfamily. The template regions have been identified on the basis of sequence conservation and structural information content. Conserved regions, recognized by permitted amino acid exchanges, are mapped on the structure and various structural features (solvent inaccessibility, secondary structure content, hydrogen bonding and residue packing) are examined. Conserved regions with high structural conservation are projected for the particular superfamily member. Interactive three-dimensional displays of the motifs in the superposed structure (in Chime® and RASMOL) are provided for better understanding and visualization. The conserved regions or templates can be projected as important signatures or minimum structural requirement for that particular superfamily. This enables the examination of single member superfamilies that provide added value to the recognition of additional members, comparative modelling and in design experiments. The database can be accessed from http://www.ncbs.res.in/~faculty/mini/SSTOSS/index.htm.

Acknowledgements

This work is supported by a Senior Research Fellowship from Wellcome Trust awarded to RS.

References

1. PASS2: a semi-automated database of protein alignments organised as structural superfamilies. Mallika V, Bhaduri A, Sowdhamini R. Nucleic Acids Res. 2002 Jan 1;30(1):284-288.
2. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995). J. Mol. Biol., 247, 536-540.

Subcategory: Protein structure

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