iDBPs

The iDBPs server predicts if a protein binds to DNA using the 3D structure of the query protein. It first predicts the functional region of the protein based on its evolutionary profile, then calculates various characteristics of the predicted functional region and global features of the protein, and finally uses a random forests classifier to predict DNA binding and estimate the confidence of the prediction. The classifier outperformed related methods, with an area under the ROC curve of 0.90 on a dataset reflecting the fraction of DNA binding proteins in a proteome.

Topic

Proteins;DNA;DNA binding sites;Protein structure analysis

Detail

  • Operation: Protein-nucleic acid binding prediction

  • Software interface: Web user interface

  • Language: -

  • License: Not stated

  • Cost: Free

  • Version name: -

  • Credit: BLOOMNET ERA-PG grant, Edmond J. Safra Bioinformatics program at Tel Aviv University, OTKA.

  • Input: -

  • Output: -

  • Contact: biosequence@tauex.tau.ac.il

  • Collection: -

  • Maturity: -

Publications

  • iDBPs: a web server for the identification of DNA binding proteins.
  • Nimrod G, et al. iDBPs: a web server for the identification of DNA binding proteins. iDBPs: a web server for the identification of DNA binding proteins. 2010; 26:692-3. doi: 10.1093/bioinformatics/btq019
  • https://doi.org/10.1093/bioinformatics/btq019
  • PMID: 20089514
  • PMC: PMC2828122

Download and documentation

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