IDDI: The Integrated Domain-Domain Interaction Analysis System

Understanding protein interactions in domain level provides valuable information about binding mechanisms and functional roles of interacting proteins. The straightforward sources of domain-domain interaction (DDI) are 3D structure of protein complexes, but the available number of 3D structures is not sufficient. The other attractive choice is to use predicted DDI datasets because plenty of such sources are available currently. Here, we developed an integrated domain-domain interaction analysis system (IDDI) that combines 23 DDI datasets and provides 204,705 unique DDIs. We determined the reliability of predicted DDIs by considering the confidence level of each prediction method, the independency of predicted datasets and the prediction scores. In comparison with other integrated DDI database, the amount of reliable DDIs is significantly increased. In addition, IDDI provides the interface for interaction analysis that enables to explore an interaction network at both protein and domain level. IDDI is freely available at http://pcode.kaist.ac.kr/iddi.