Integrative approach for computationally inferring protein domain interactions.
BACKGROUND
The current need for high-throughput protein interaction detection has resulted in interaction data being generated en masse through such experimental methods as yeast-two-hybrids and protein chips. Such data can be erroneous and they often do not provide adequate functional information for the detected interactions. Therefore, it is useful to develop an in silico approach to further validate and annotate the detected protein interactions.


RESULTS
Given that protein-protein interactions involve physical interactions between protein domains, domain-domain interaction information can be useful for validating, annotating, and even predicting protein interactions. However, large-scale, experimentally determined domain-domain interaction data do not exist. Here, we describe an integrative approach to computationally derive putative domain interactions from multiple data sources, including protein interactions, protein complexes, and Rosetta Stone sequences. We further prove the usefulness of such an integrative approach by applying the derived domain interactions to predict and validate protein-protein interactions.


BACKGROUND
A database of putative protein domain interactions derived using the method described in this paper is available at http://interdom.lit.org.sg.
Ng
See-Kiong
SK
Laboratories for Information Technology, 21 Heng Mui Keng Terrace, Singapore 119613. skng@lit.org.sg
Zhang
Zhuo
Z
Tan
Soon-Heng
SH
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D003628:Database Management Systems; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry; D016247:Information Storage and Retrieval / Q000379:methods; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D018511:Systems Integration
D005656:Fungal Proteins; D011506:Proteins