| Method | Features | Training methods | Reference | Web link |
| BindN
| Side chain pKa value,Hydrophobicity index , Molecular mass
| Support vector machine
| Wang,L. and Brown,S.J. (2006) BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res., 34, W243-W248.
| http://bioinformatics.ksu.edu/bindn/
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| BindN+
| Biochemical features, Evolutionary information
| Support vector machine
| Wang,L., Huang,C., Yang,M.Q and Yang,J.Y (2010) BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features, BMC Systems Biology, 4(Suppl 1), S3.
| http://bioinfo.ggc.org/bindn+/
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| NAPS
| Amino acid properties, Evolutionary information
| C4.5 algorithm with boot-strap aggregation and cost-sensitive learning
| Carson,M.B., Langlois,R. and Lu,H. (2010) NAPS: a residue-level nucleic acid-binding prediction server, Nucleic Acids Research,38, W431-W435.
| http://proteomics.bioengr.uic.edu/NAPS
|
| Pprint
| PSSM profile
| Support vector machine
| Kumar, M., Gromiha, M.M. and Raghava, G.P.S. (2008) Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins: Structure, Function and Bioinformatics,71, 189-94
| http://www.imtech.res.in/raghava/pprint/
|
| RNABindR v2.0
| PSSM profile
| Support vector machine
| Walia, R.R., Caragea, C., Lewis, B.A., Towfic, F., Terribilini, M., El-Manzalawy, Y., Dobbs, D., Honavar, V. (2012) Protein-RNA Interface Residue Prediction using Machine Learning: An Assessment of the State of the Art. BMC Bioinformatics, 13:89
| http://einstein.cs.iastate.edu/RNABindR/
|
| RNAProB
| Smoothed PSSM profile
| Support vector machine
| Cheng CW, Su EC, Hwang JK, Sung TY, Hsu WL. (2008) Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics. 9 Suppl 12:S6.
| Standalone
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