NAR Molecular Biology Database Collection entry number 829
Pugalenthi G., Bhaduri A. and Sowdhamini R.
National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Ballary Road, Bangalore 560 065, India
Structural motifs are central to the integrity of the fold and require careful analysis for their identification. IMOTdb is a repertoire of spatially interacting motifs in single protein structures as well as those among distantly related protein structures that belong to a superfamily. iMotdb pertains to 854 488 motifs of 60 849 protein structural domains corresponding to SCOP 1.67 database. For each structural member in the superfamily that has been considered in SCOP database, homologous sequences are individually identified. Alignment positions are provided an average similarity score after consulting amino acid exchange matrix. Contiguous residues with an average similarity score of more than 50 are treated as conserved residues or motifs. These motifs are mapped on to the structural superfamily member to examine their spatial proximity with each other. Pairs of conserved residues are further examined by calculating psuedoenergies that describe the strength of interactions. Spatially interacting motifs are mapped on to the alignment of the superfamily to further recognize spatially interacting motifs that are conserved throughout the superfamily. Interactive three-dimensional display of the motifs on the structure is provided for better understanding and visualization. Structural information about individual motifs is provided that includes the presence of motifs in secondary structures, solvent accessibility patterns and positional variations amongst superfamily members (reflected as root mean square deviations). Spatially interacting motifs can be critical for structure and/or function. They are useful in searching for distant homologues and establishing remote homologies among the largely unassigned sequences in genome databases. Availability of information on structural motifs in large number of protein structures should be useful as starting points to perform detailed analysis, for the rational design of experiments in protein folding, site-directed mutagenesis and to understand mechanism of action and conformational changes in proteins. iMOTdb database can be accessed from http://caps.ncbs.res.in/imotdb/.
Category: Structure Databases
Subcategory: Protein structure
Category: Metabolic and Signaling Pathways
Subcategory: Protein-protein interactions
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