The interacting motif database or iMOTdb , lists interacting motifs that
are identified for all structural entries in the PDB. The conserved
patterns or finger prints are identified for individual structural
entries and also grouped together for reporting the common motifs shared
among all superfamily members. The iMOT package (Bhaduri et al., 2004 ) has been employed for identifying the motifs in the database.
Interacting motifs has been shown to assist our understanding of
proteins structure and function. Information on such motifs should be of
valuable in protein folding, modeling and engineering experiments. As
shown in previous studies conserved spatially interacting motifs act as
important constraint in pattern based remote homology search methods
(Bhaduri et al., 2004 ). The iMOT DB is provided with links to aid sequence search
protocol using PHI-BLAST (Zhang et al, 1998) and SCAN MOT (Chakrabarti., et al., 2005)
employing the interacting motifs.
The interacting motifs representing the superfamilies of proteins are
derived from structural alignments obtained from PASS2 (Bhaduri et al., 2004 ).
These motifs are finger prints for a given
protein family and provides useful insights regarding the structural and
functional role regarding the protein. Pseudo potential evaluated
between the various pairs of motifs reflects the interacting strength
between the regions and highlights the thermodymanic stability of the
local substructure. The database would thus provide useful insight into
the understanding of the folding, structural modeling and envisaging
mutational exercise on a given polypeptide.
1. Bhaduri, A., Pugalenthi, G., Gupta, N. and Sowdhamini, R. (2004). iMOT: an interactive package for the selection of spatially interacting motifs. Nucleic Acids Research 32, W602-W605
2. Bhaduri.A., Ravishankar, R. and Sowdhamini, R. (2004). Conserved spatially interacting motifs of protein superfamilies: Application to fold recognition and function annotation of genome data. Proteins, 54(4), 657-70.
3. Saikat Chakrabarti., Prem Anand., Nitin Bhardwaj., Pugalenthi, G. and Sowdhamini, R.(2005) SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motif. Nucleic Acid Res., 33, 274-276.
4. Bhaduri, A., Pugalenthi, G. and Sowdhamini, R. (2004). PASS2: an automated database of protein alignments organised as structural superfamilies. BMC Bioinformatics 5:35
5. Zhang Z, Schaffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV,
Altschul SF. (1998): Protein sequence similarity searches using patterns as seeds.
Nucleic Acids Res., 26(17):3986-3990.