SMotif

SMotif is a server to identify set of structural motifs from protein structures. Such motifs among structurally aligned proteins are recognized by the conservation of amino acid preference and solvent inaccessibility and are examined for the conservation of other important structural features like secondary structural content, hydrogen bonding pattern and residue packing.

Method:

An automated method has been developed that identify protein segments, which form the conserved core in homologous proteins, using conservation of amino acid exchange, solvent inaccessibility, secondary structural content, hydrogen bonding pattern and residue packing.

A structural feature is considered conserved at an alignment position if it is present in all or all but-one members within the alignment. The identified structural motifs are mapped on the alignment using different color code. Ranking of the motifs is done considering the extent of conservation of the structural feature. A flavor of the three-dimensional orientation of the structural motifs is provided via graphic displays and spatial orientation matrices.

Please click here for different input option usage.


Reference

Chakrabarti, S., Venkataramanan, K., and Sowdhamini, R. (2003) SMoS: A database of Structural Motifs of Superfamily. Protein Eng. 16, 791-3.

Chakrabarti, S, and Sowdhamini, R. (2003) Regions of minimal structural variation among members of protein domain superfamilies: Application to remote homology detection and modeling using distant relationships. FEBS Letters. 569, 31-6.

Chakrabarti S., et al. (2006) SSToSS - Sequence-Structural Templates of Single-member Superfamilies. In Silico Biol. 6, 0029.

Apweiler,R., et al. (1997). Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT, TREMBL. Proceedings of the 5th International Conference on ISMB, pp. 33-43.

Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.

Berman, H.M. et al. (2000). The Protein Data Bank. Nucleic Acids Res., 28, 235-242.

Johnson M.S., et al. (1993) Alignment and searching for common protein folds using a data bank of structural templates. J. Mol. Biol., 231, 735-752.

Russell, R. B. and Barton, G.J. (1994) Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side chain contacts secondary structure and accessibility. J Mol Biol., 244, 332-350.

Contact:

Dr. R. Sowdhamini (mini@ncbs.res.in)

Dr. Saikat Chakrabarti

Dr. PN. Suganthan

G. Pugalenthi