The interacting motif database or iMOTdb , lists interacting motifs thatare 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.
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