iMOT

iMOT identifies spatially interacting motifs among proteins with similar three-dimensional structures to detect conserved functional regions and infer remote homology despite low overall sequence identity.

Key Features:

• Automatic Identification: Automates detection of conserved regions by evaluating spatial interactions between stretches of amino acids.
• Pseudo-potential Calculations: Employs pseudo-potentials to quantify interaction strengths between conserved motifs.
• Remote Homology Detection: Enables identification of distant homologues by focusing on interacting motifs conserved despite sequence divergence and not apparent in genome database classifications.

Scientific Applications:

• Protein Folding and Modelling: Provides motif-level interaction data to inform understanding of folding mechanisms and computational modelling.
• Protein Engineering: Identifies conserved interactive regions that can guide protein engineering experiments to modify or design proteins with desired properties.
• Genomic Research: Assists classification and functional inference of unassigned genomic sequences based on structural and motif-level similarities.

Methodology:

Detects conserved stretches within protein structures and evaluates their spatial interactions; uses pseudo-potential calculations to quantify motif interaction strengths, leveraging the concept that functional selection and three-dimensional structural constraints preserve sequence similarity among proteins with similar folds despite evolutionary divergence.