Programs

Year Program Website

RBP-sequence based

2006 BindN1 http://bioinfo.ggc.org/bindn/
2007 RNABindR2 http://einstein.cs.iastate.edu/RNABindR/
2008 PPRInt3 http://www.imtech.res.in/raghava/pprint/
2008 RNAproB4 NA
2008 PRINTR5 http://210.42.106.80/printr/
2008 RISP6 http://grc.seu.edu.cn/RISP
2009 PiRaNhA7 http://www.bioinformatics.sussex.ac.uk/PIRANHA
2010 BindN+8 http://bioinfo.ggc.org/bindn+/
2010 NAPS9 http://proteomics.bioengr.uic.edu/NAPS/
2010 PRBR10 http://www.cbi.seu.edu.cn/PRBR/optional.php
2011 Sungwook11 NA
2011 SRCPred12 http://tardis.nibio.go.jp/netasa/srcpred/
2011 Predict_RBP13 http://cic.scu.edu.cn/bioinformatics/Predict_RBP.rar
2011 meta214 https://genesilico.pl/meta2
2012 Qian-Zhong15 NA
2014 RNABindRPlus16 http://einstein.cs.iastate.edu/RNABindRPlus/
2015 RBRIdent17 http://166.111.152.91/RBRIdent

RBP-structure based

2006 KYG18 http://cib.cf.ocha.ac.jp/KYG/
2008 RsiteDB19 http://bioinfo3d.cs.tau.ac.il/RsiteDB/
2008 DR_bind120 http://drbind.limlab.ibms.sinica.edu.tw/
2009 PRIP21 http://www.qfab.org/PRIP
2010 OPRA22 NA
2011 DRNA23 NA
2010 Struct-NB24 NA
2010 PRNA25 http://doc.aporc.org/wiki/PRNA
2014 aaRNA26 http://sysimm.ifrec.osaka-u.ac.jp/aarna/
2014 RBRDetector27 http://ibi.hzau.edu.cn/rbrdetector
2014 Xiaoyong28 NA

DBP-sequence based

2015 RBscore29 http://ahsoka.u-strasbg.fr/rbscore/
2004 DBS-Pred30 http://www.abren.net/dbs-pred/
2005 DBS-PSSM31 http://www.abren.net/dbs-pssm/
2006 DNABindR32 NA
2007 DISIS33 http://cubic.bioc.columbia.edu/services/disis
2007 DP-Bind34 http://lcg.rit.albany.edu/dp-bind/
2009 ProteDNA35 http://protedna.csbb.ntu.edu.tw/
2009 DbindR36 http://www.cbi.seu.edu.cn/DBindR/DBindR.htm
2009 SDCPred37 http://sdcpred.netasa.org/
2014 Byungkyu38 NA

DBP-structure based

1999 Hidetoshi39 NA
2003 Susan40 NA
2005 DBS-kernel41 NA
2005 Pro-dna42 http://bioinformatics.bioengr.uic.edu/pro-dna/
2005 PreDs43 http://pre-s.protein.osaka-u.ac.jp/~preds/
2007 DISPLAR44 http://pipe.scs.fsu.edu/displar.html
2007 DR_bind145 http://drbind.limlab.ibms.sinica.edu.tw/
2008 DBD-Hunter46 http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/
2010 DNABINDPROT47 http://www.prc.boun.edu.tr/appserv/prc/dnabindprot/
2011 metaDBSite48 http://projects.biotec.tu-dresden.de/metadbsite/
2011 Xiong49 NA
2012 Sucharita50 NA
2013 Duo-Duo51 NA
2013 PreDNA52 http://202.207.14.178/predna/
2013 DNABind53 http://mleg.cse.sc.edu/DNABind/
2014 Bi-Qing54 NA

References:

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  • 3.Kumar, M., Gromiha, A.M. and Raghava, G.P.S. (2008) Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins, 71, 189-194.
  • 4.Cheng, C.W., Su, E.C.Y., Hwang, J.K., Sung, T.Y. and Hsu, W.L. (2008) Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. Bmc Bioinformatics, 9.
  • 5.Wang, Y., Xue, Z., Shen, G. and Xu, J. (2008) PRINTR: Prediction of RNA binding sites in proteins using SVM and profiles. Amino Acids, 35, 295-302.
  • 6.Tong, J., Jiang, P. and Lu, Z.H. (2008) RISP: A web-based server for prediction of RNA-binding sites in proteins. Comput Meth Prog Bio, 90, 148-153.
  • 7.Murakami, Y., Spriggs, R.V., Nakamura, H. and Jones, S. (2010) PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. Nucleic Acids Research, 38, W412-W416.
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  • 9.Carson, M.B., Langlois, R. and Lu, H. (2010) NAPS: a residue-level nucleic acid-binding prediction server. Nucleic Acids Research, 38, W431-W435.
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  • 15.Li, T. and Li, Q.Z. (2012) Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure. J Theor Biol, 312, 55-64.
  • 16.Walia, R.R., Xue, L.C., Wilkins, K., El-Manzalawy, Y., Dobbs, D. and Honavar, V. (2014) RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins. Plos One, 9.
  • 17.Xiong, D., Zeng, J. and Gong, H. (2015) RBRIdent: An algorithm for improved identification of RNA-binding residues in proteins from primary sequences. Proteins, 83, 1068-1077.
  • 18.Kim, O.T.P., Yura, K. and Go, N. (2006) Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Research, 34, 6450-6460.
  • 19.Shulman-Peleg, A., Shatsky, M., Nussinov, R. and Wolfson, H.J. (2008) Prediction of interacting single-stranded RNA bases by protein-binding patterns. J Mol Biol, 379, 299-316.
  • 20.Chen, Y.C. and Lim, C. (2008) Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res, 36.
  • 21.Maetschke, S.R. and Yuan, Z. (2009) Exploiting structural and topological information to improve prediction of RNA-protein binding sites. Bmc Bioinformatics, 10.
  • 22.Perez-Cano, L. and Fernandez-Recio, J. (2010) Optimal Protein-RNA Area, OPRA: A propensity-based method to identify RNA-binding sites on proteins. Proteins, 78, 25-35.
  • 23.Zhao, H.Y., Yang, Y.D. and Zhou, Y.Q. (2011) Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Research, 39, 3017-3025.
  • 24.Towfic, F., Caragea, C., Gemperline, D.C., Dobbs, D. and Honavar, V. (2010) Struct-NB: predicting protein-RNA binding sites using structural features. Int J Data Min Bioin, 4, 21-43.
  • 25.Liu, Z.P., Wu, L.Y., Wang, Y., Zhang, X.S. and Chen, L.N. (2010) Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics, 26, 1616-1622.
  • 26.Li, S., Yamashita, K., Amada, K.M. and Standley, D.M. (2014) Quantifying sequence and structural features of protein-RNA interactions. Nucleic Acids Res.
  • 27.Yang, X.X., Deng, Z.L. and Liu, R. (2014) RBRDetector: improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies. Proteins, 82, 2455-2471.
  • 28.Pan, X., Zhu, L., Fan, Y.-X. and Yan, J. (2014) Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection. Computational Biology and Chemistry, 53, Part B, 324-330.
  • 29.Miao, Z. and Westhof, E. (2015) Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score. Nucleic Acids Res.
  • 30.Ahmad, S., Gromiha, M.M. and Sarai, A. (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 20, 477-486.
  • 31.Ahmad, S. and Sarai, A. (2005) PSSM-based prediction of DNA binding sites in proteins. Bmc Bioinformatics, 6.
  • 32.Yan, C.H., Terribilini, M., Wu, F.H., Jernigan, R.L., Dobbs, D. and Honavar, V. (2006) Predicting DNA-binding sites of proteins from amino acid sequence. Bmc Bioinformatics, 7.
  • 33.Ofran, Y., Mysore, V. and Rost, B. (2007) Prediction of DNA-binding residues from sequence. Bioinformatics, 23, I347-I353.
  • 34.Hwang, S., Gou, Z.K. and Kuznetsov, I.B. (2007) DP-Bind: a Web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics, 23, 634-636.
  • 35.Chu, W.Y., Huang, Y.F., Huang, C.C., Cheng, Y.S., Huang, C.K. and Oyang, Y.J. (2009) ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. Nucleic Acids Res, 37, W396-W401.
  • 36.Wu, J.S., Liu, H.D., Duan, X.Y., Ding, Y., Wu, H.T., Bai, Y.F. and Sun, X. (2009) Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics, 25, 30-35.
  • 37.Andrabi, M., Mizuguchi, K., Sarai, A. and Ahmad, S. (2009) Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks. Bmc Struct Biol, 9.
  • 38.Park, B., Im, J., Tuvshinjargal, N., Lee, W. and Han, K. (2014) Sequence-based prediction of protein-binding sites in DNA: Comparative study of two SVM models. Comput Meth Prog Bio, 117, 158-167.
  • 39.Kono, H. and Sarai, A. (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins-Structure Function And Genetics, 35, 114-131.
  • 40.Jones, S., Shanahan, H.P., Berman, H.M. and Thornton, J.M. (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res, 31, 7189-7198.
  • 41.Bhardwaj, N., Langlois, R.E., Zhao, G.J. and Lu, H. (2005) Kernel-based machine learning protocol for predicting DNA-binding proteins. Nucleic Acids Research, 33, 6486-6493.
  • 42.Bhardwaj, N. and Lu, H. (2007) Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions. Febs Lett, 581, 1058-1066.
  • 43.Tsuchiya, Y., Kinoshita, K. and Nakamura, H. (2005) PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics, 21, 1721-1723.
  • 44.Tjong, H. and Zhou, H.X. (2007) DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Research, 35, 1465-1477.
  • 45.Chen, Y.C., Wu, C.Y. and Lim, C. (2007) Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation. Proteins, 67, 671-680.
  • 46.Gao, M. and Skolnick, J. (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Research, 36, 3978-3992.
  • 47.Ozbek, P., Soner, S., Erman, B. and Haliloglu, T. (2010) DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Res, 38, W417-W423.
  • 48.Si, J.N., Zhang, Z.M., Lin, B.Y., Schroeder, M. and Huang, B.D. (2011) MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. Bmc Syst Biol, 5.
  • 49.Xiong, Y., Liu, J. and Wei, D.Q. (2011) An accurate feature-based method for identifying DNA-binding residues on protein surfaces. Proteins, 79, 509-517.
  • 50.Dey, S., Pal, A., Guharoy, M., Sonavane, S. and Chakrabarti, P. (2012) Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters. Nucleic Acids Research, 40, 7150-7161.
  • 51.Wang, D.D., Li, T.H., Sun, J.M., Li, D.P., Xiong, W.W., Wang, W.Y. and Tang, S.N. (2013) Shape string: A new feature for prediction of DNA-binding residues. Biochimie, 95, 354-358.
  • 52.Li, T., Li, Q.Z., Liu, S., Fan, G.L., Zuo, Y.C. and Peng, Y. (2013) PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information. Bioinformatics, 29, 678-685.
  • 53.Liu, R. and Hu, J. (2013) DNABind: a hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches. Proteins, 81, 1885-1899.
  • 54.Li, B.Q., Feng, K.Y., Ding, J. and Cai, Y.D. (2014) Predicting DNA-binding sites of proteins based on sequential and 3D structural information. Mol Genet Genomics, 289, 489-499.