iDBPs: a web server for the identification of DNA binding proteins

• Published in: Bioinformatics Vol. 26; no. 5; pp. 692 - 693
• Main Authors: Nimrod, Guy, Schushan, Maya, Szilágyi, András, Leslie, Christina, Ben-Tal, Nir
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.03.2010
• Subjects: Applications Note; Binding; Binding Sites; Bioinformatics; Biological and medical sciences; Classifiers; Clusters; Databases, Protein; Deoxyribonucleic acid; DNA-Binding Proteins - chemistry; Fundamental and applied biological sciences. Psychology; General aspects; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Proteins; Query processing; Sequence Analysis, Protein; Servers; Software; Binding protein; Identification; DNA; DNA binding protein; World wide web
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btq019

The iDBPs server uses the three-dimensional (3D) structure of a query protein to predict whether it binds DNA. First, the algorithm predicts the functional region of the protein based on its evolutionary profile; the assumption is that large clusters of conserved residues are good markers of functional regions. Next, various characteristics of the predicted functional region as well as global features of the protein are calculated, such as the average surface electrostatic potential, the dipole moment and cluster-based amino acid conservation patterns. Finally, a random forests classifier is used to predict whether the query protein is likely to bind DNA and to estimate the prediction confidence. We have trained and tested the classifier on various datasets and shown that it outperformed related methods. On a dataset that reflects the fraction of DNA binding proteins (DBPs) in a proteome, the area under the ROC curve was 0.90. The application of the server to an updated version of the N-Func database, which contains proteins of unknown function with solved 3D-structure, suggested new putative DBPs for experimental studies. Availability: http://idbps.tau.ac.il/ Contact: NirB@tauex.tau.ac.il Supplementary information: Supplementary data are available at Bioinformatics online.