DIMA domain interaction map

DIMA domain interaction map maps functional and physical interactions among conserved protein domains by integrating experimental structural data and computational predictions.

Key Features:

• Comprehensive Domain Coverage: Uses SIMAP (Similarity Matrix of Proteins) to profile 7,038 Pfam domains across 460 completely sequenced genomes.
• Integration of Experimental Data: Incorporates iPfam (3,074 interacting domain pairs from solved structures) and 3did (3,034 contact pairs), yielding 3,653 distinct interacting domain pairs.
• Computational Predictions: Applies a domain pair exclusion algorithm to 83,969 IntAct protein-protein interactions to obtain 21,513 domain pairs and applies the same approach to STRING predicted interactions to obtain 2,378 additional interacting domain pairs.
• Algorithmic Approaches: Employs two different algorithms for predicting domain-domain interactions, including a domain pair exclusion algorithm.

Scientific Applications:

• Functional relationship identification: Infers potential functional links between proteins by mapping interacting domain pairs.
• Structural interpretation of protein-protein interactions: Relates experimentally derived domain contacts from iPfam and 3did to domain interaction hypotheses.
• Evolutionary conservation analysis: Enables exploration of conserved domain interactions across 460 genomes.
• Drug discovery targeting: Supports identification of specific domain interactions as potential therapeutic targets.

Methodology:

Combines experimental structural data with computational prediction using SIMAP for domain hits, phylogenetic profiling, domain pair exclusion algorithms, integration of iPfam, 3did, IntAct, and STRING, and two prediction algorithms.