SSToSS - Sequence-structural templates of single-member superfamilies

Saikat Chakrabarti, Gowri Manohari, Ganesan Pugalenthi, Ramanathan Sowdhamini

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)311-319
Number of pages9
JournalIn Silico Biology
Volume6
Issue number4
StatePublished - 2006
Externally publishedYes

Keywords

  • Comparative modeling
  • Conserved regions
  • Distant similarity
  • Motif-based database search
  • Protein structure prediction
  • Spatial orientation of motifs
  • Superfamily signatures

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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