IDDI: integrated domain-domain interaction and protein interaction analysis system

Abstract

BackgroundDeciphering protein-protein interaction (PPI) in domain level enriches valuable information about binding mechanism and functional role of interacting proteins. The 3D structures of complex proteins are reliable source of domain-domain interaction (DDI) but the number of proven structures is very limited. Several resources for the computationally predicted DDI have been generated but they are scattered in various places and their prediction show erratic performances. A well-organized PPI and DDI analysis system integrating these data with fair scoring system is necessary.MethodWe integrated three structure-based DDI datasets and twenty computationally predicted DDI datasets and constructed an interaction analysis system, named IDDI, which enables to browse protein and domain interactions with their relationships. To integrate heterogeneous DDI information, a novel scoring scheme is introduced to determine the reliability of DDI by considering the prediction scores of each DDI and the confidence levels of each prediction method in the datasets, and independencies between predicted datasets. In addition, we connected this DDI information to the comprehensive PPI information and developed a unified interface for the interaction analysis exploring interaction networks at both protein and domain level.ResultIDDI provides 204,705 DDIs among total 7,351 Pfam domains in the current version. The result presents that total number of DDIs is increased eight times more than that of previous studies. Due to the increment of data, 50.4% of PPIs could be correlated with DDIs which is more than twice of previous resources. Newly designed scoring scheme outperformed the previous system in its accuracy too. User interface of IDDI system provides interactive investigation of proteins and domains in interactions with interconnected way. A specific example is presented to show the efficiency of the systems to acquire the comprehensive information of target protein with PPI and DDI relationships. IDDI is freely available at http://pcode.kaist.ac.kr/iddi/.

Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs

“…The amino acid sequences of non-redundant preliminary PPIs were extracted and domains were assigned to them using Pfam version 27.0 62 . The list of non-redundant domain-domain interactions was prepared from the meta-databases Domine 63 , DIMA 3.0 64 and IDDI database 65 . These use complexes available in the Protein Data Bank (PDB) 66 to identify by interacting domains the Pfam families containing these domains.…”

HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis

“…For the prediction of functional associations between genes in humans, we selected six types of evidence, which were collected from seven public databases for the years prior to 2018, including 22,004 expression pro les (Coxpresdb) [12], 288,375 gene annotations (GOC) [13], 59,617 subcellular gene localizations (Compartments) [14], 156,859 domain interactions (IDDI [15] and Pfam [16]), 20,567 phylogenetic pro les (DIOPT) [17] , and 9,220 human proteins and proteins from Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, and Schizosaccharomyces pombe used to compute interologs (Inparanoid) [18] (Fig. 1).…”

Prediction of Scaffold Proteins based on Protein Interaction and Domain Architectures

“…The protein domain information were taken from the Pfam database [10]. PPI and DDI data were collected from integrated PPI database [11] and integrated DDI database (IDDI) [12] respectively. Moreover, we downloaded the protein complex datasets from COFECO [13].…”