MegaMotifbase: Structural Motifs Database
MegaMotifbase is a database of structural motifs for protein structures related at the family and/or superfamily level. 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. These motifs may form the common core by maintaining a particular spatial orientation pattern when compared across different proteins belonging to the same family or superfamily. Such motifs can also be employed to design and rationalize protein engineering and folding experiments. Therefore, the MegaMotifbase can be a useful resource to gain knowledge about structure and functional relationship of proteins.
MegaMotifbase provides a comprehensive compilation of structural motifs identified through a completely automated method for large number of families (1032) and superfamilies (1194) of proteins.
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. MegaMotifbase also provides three-dimensional orientation patterns of the identified motifs in terms of inter-motif distances and torsion angles. Important applications of structural motifs are also provided in several crucial areas such as similar sequence and structure search, multiple sequence alignment and homology modeling.
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.
Chakrabarti S., et al. (2006) SSToSS - Sequence-Structural Templates of Single-member Superfamilies. In Silico Biol. 6, 0029
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
