SMoS.2: Update of database of Structural Motifs in Superfamilies


NAR Molecular Biology Database Collection entry number 1756
Anita Rachel Chacko, Oommen K. Mathew, Adwait Joshi, Upadhyayula Surya Raghavender and R. Sowdhamini
National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK campus, Bangalore 560065, India

Database Description

Remote homology detection, namely the accumulation of reliable but distantly related sequences of a protein family, remains a challenging problem in biology. Early realisation of such relationships can provide clues on evolutionary trends and to attribute function to newly recognised families and gene products. Conserved and solvent-buried regions are usually strong signatures and we refer to them as structural motifs. We had earlier shown that it is possible to employ structural motifs as constraints in sequence searches to improve coverage without compensating on sensitivity or computational time.

Recent Developments

We have recently performed an update of structural motifs in protein domain superfamilies and in correspondence with our database of structure-based sequence alignment of protein domain superfamilies. This version of the SMoS database provides an immediate glimpse on structural motifs for nearly 1000 superfamilies, where they are mapped on the alignment as well as on the structures. The updated version of SMoS database can be accessed from http://caps.ncbs.res.in/SMoS2/

References

1. Bhaduri, A., Pugalenthi, G. & Sowdhamini, R.(2004) PASS2: an automated database of protein alignments organised as structural superfamilies . BMC Bioinformatics, 5, 35.
2. Adwait Govind Joshi, Upadhyayula Surya Raghavender and Ramanathan Sowdhamini. (2013) Improved performance of sequence search algorithms in remote homology detection. f1000 Research (in press)
3. Chakrabarti S, Venkatramanan K, Sowdhamini R.(2003) SMoS: a database of structural motifs of protein superfamilies. Protein Eng.,16(11),791-793.
4. Gandhimathi, A., Nair, A. and Sowdhamini, R. (2011) PASS2.4: An update of database of structure-based sequence alignments of structural domain superfamilies. Nucleic Acids Research. 2011:1–4

Subcategory: Protein structure

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