Protein–DNA interaction site predictor

Web servers

Structure- and sequence-based prediction of DNA-binding sites in DNA-binding proteins can be performed on several web servers listed below. DISIS predicts DNA binding sites directly from the 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. DISIS2 receives the raw amino acid sequence and generates all features from it, such as secondary structure, solvent accessibility, disorder, b-value, protein-protein interaction, coiled coils, and evolutionary profiles, etc. The amount of predicted features is much larger than of DISIS (previous version). Finally, DISIS2 is able to predict DNA-binding residues from protein sequence of DNA-binding proteins. DNABindR predicts DNA binding sites from amino acid sequences using machine learning algorithms. DISPLAR makes a prediction based on properties of protein structure. Knowledge of the protein structure is required BindN makes a prediction based on chemical properties of the input protein sequence. Knowledge of the protein structure is not required. BindN+ is an upgraded version of BindN that applies support vector machines (SVMs) to sequence-based prediction of DNA or RNA-binding residues from biochemical features and evolutionary information. 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. DBS-PSSM and DBS-Pred predict the DNA-binding in a protein from their sequence information.

References

References

1. (2007). "Prediction of DNA-binding residues from sequence". [[Bioinformatics (journal).
2. (2006). "Predicting DNA-binding sites of proteins from amino acid sequence". [[BMC Bioinformatics]].
3. (2007). "DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces". [[Nucleic Acids Research]].
4. (July 2006). "BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences". Nucleic Acids Res..
5. (2010). "BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features". [[BMC Systems Biology]].
6. (2007). "DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins". [[Bioinformatics (journal).
7. (2005). "PSSM based prediction of DNA-binding sites in proteins". [[BMC Bioinformatics]].
8. (2004-01-22). "Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information". Oxford University Press (OUP).