Protein-DNA interaction site predictor

Structural and physical properties of DNA provide important constraints on the binding sites formed on surfaces of DNA-binding proteins. Characteristics of such binding sites may be used for predicting DNA-binding sites from the structural and even sequence properties of unbound proteins. This approach has been successfully implemented for predicting the protein-protein interface. Here, this approach is adopted for predicting DNA-binding sites in DNA-binding proteins. First attempt to use sequence and evolutinary features to predict DNA-binding sites in proteins was made by Ahmad et al. (2004) and Ahmad and Sarai (2005). Some methods use structural information to predict DNA-binding sites and therefore require a 3-dimensional structure of the protein, while others use only sequence information and do not require protein structure in order to make a prediction. Structure- and sequence-based prediction of DNA-binding sites in DNA-binding proteins can be performed on several web servers listed below:

1) DISIS predicts DNA binding sites directly from amino acid sequence and hence is applicable for all known proteins. It is based on the chemical-physical properties of the residue and its environment, predicted structural features and evolutionary data. It uses machine learning algorithms. Ofran , Y. Mysore , V. and Rost B. Prediction of DNA-binding residues from sequence Bioinformatics 23(13):i347-53 (2007)]

2) DISPLAR makes a prediction based on properties of protein structure. Knowledge of the protein structure is required Tjong , H. and Zhou, H.-X. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Research 35:1465-1477 (2007)]

3) BindN makes a prediction based on chemical properties of the input protein sequence. Knowledge of the protein structure is not required. L. Wang, and S. J. Brown. "BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences." Nucleic Acids Research. 2006 Jul 1;34(Web Server issue):W243-8. PMID 16845003]

4) DP-Bind combines multiple methods to make a consensus prediction based on the profile of evolutionary conservation and properties of the input protein sequence. Profile of evolutionary conservation is automatically generated by the web-server. Knowledge of the protein structure is not required. Hwang, S , Gou, Z and Kuznetsov, I.B. "DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins" Bioinformatics 2007 23(5):634-636 PMID 17237068 ]

5) DBS-PSSM PSSM based prediction of DNA-binding sites in proteins, Shandar Ahmad and Akinori Sarai, BMC Bioinformatics 6:33 (2005)] (This article also shows how prediction can be significantly sped up by generating alignments against limited data sets).

6) DBS-Pred Analysis and Prediction of DNA-binding proteins and their binding　residues based on Composition, Sequence and Structural Information, Shandar Ahmad , M. Michael Gromiha and Akinori Sarai, Bioinformatics 20 (2004), 477-486] (This artcile also uses amino acid composition analysis to predict DNA-binding proteins, and uses structure information to improve binding site prediction. Method is based on single sequences only and thousands of proteins can be processed in less than an hour). Standalone is also available.

ee also

References

External links

* [http://cubic.bioc.columbia.edu/services/disis DISIS] search engine site at Columbia University
* [http://pipe.scs.fsu.edu/displar.html DISPLAR] search engine site at Florida State University
* [http://bioinformatics.ksu.edu/bindn/ BindN] search engine site at Kansas State University
* [http://lcg.rit.albany.edu/dp-bind DP-Bind] search engine site at State University of New York at Albany
* [http://www.netasa.org/dbs-pred] DBS-Pred (2004)
* [http://www.netasa.org/dbs-pssm] DBS-PSSM (2005)
* Software for DNA modeling - [http://www.agilemolecule.com/Ascalaph/Ascalaph_DNA.html Ascalaph DNA]

Protein-protein interaction prediction