iMOT is an automated method for identifying conserved spatially interacting regions across proteins. Signatures of proteins are derived based on spatial interactions among sequentially conserved regions. Interactions of the conserved stretches are evaluated based on pseudo-energies. Details of the method are provided in the help page.

Spatially interacting motifs act as a superset for all functionally important and structural invariant regions in proteins. They are of potential use in protein engineering and modeling experiments since they may be crucial features for structural stability and biochemical function thus forming an integral part of the protein. Interacting motifs have been shown to be useful in searching distant homologues and establishing remote homologies among large unassigned sequences in the genome databases.

1 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.

2 Chakrabarti, S., John, J. and Sowdhamini, R. (2004). Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints. J Mol Model (Online). 10, 69-75.