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Volumn 9, Issue 1, 2014, Pages

Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; RNA BINDING PROTEIN; AMINO ACID; DNA;

EID: 84899864030     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086703     Document Type: Article
Times cited : (174)

References (63)
  • 1
    • 20544460658 scopus 로고    scopus 로고
    • Protein-DNA recognition patterns and predictions
    • DOI 10.1146/annurev.biophys.34.040204.144537
    • Sarai A, Kono H (2005) Protein-DNA recognition patterns and predictions. Annu Rev Biophys Biomol Struct 34: 379-398. doi:10.1146/annurev.biophys.34. 040204.144537. (Pubitemid 40847730)
    • (2005) Annual Review of Biophysics and Biomolecular Structure , vol.34 , pp. 379-398
    • Sarai, A.1    Kono, H.2
  • 2
    • 84865283412 scopus 로고    scopus 로고
    • Atomistic modeling of protein-DNA interaction specificity: Progress and applications
    • doi:10.1016/j.sbi.2012.06.002
    • Liu LA, Bradley P (2012) Atomistic modeling of protein-DNA interaction specificity: progress and applications. Curr Opin Struct Biol 22: 397-405. doi:10.1016/j.sbi.2012.06.002.
    • (2012) Curr Opin Struct Biol , vol.22 , pp. 397-405
    • Liu, L.A.1    Bradley, P.2
  • 3
    • 77953693713 scopus 로고    scopus 로고
    • Boosting the prediction and understanding of DNA-binding domains from sequence
    • doi:10.1093/nar/gkq061
    • Langlois RE, Lu H (2010) Boosting the prediction and understanding of DNA-binding domains from sequence. Nucleic Acids Res 38: 3149-3158. doi:10.1093/nar/gkq061.
    • (2010) Nucleic Acids Res , vol.38 , pp. 3149-3158
    • Langlois, R.E.1    Lu, H.2
  • 4
    • 0024396714 scopus 로고
    • 4-Hydroxynonenal induces a DNA-binding protein similar to the heat-shock factor
    • Cajone F, Salina M, Benelli-Zazzera A (1989) 4-Hydroxynonenal induces a DNA-binding protein similar to the heat-shock factor. Biochem J 262: 977-979. (Pubitemid 19225174)
    • (1989) Biochemical Journal , vol.262 , Issue.3 , pp. 977-979
    • Cajone, F.1    Salina, M.2    Benelli-Zazzera, A.3
  • 5
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • DOI 10.1016/j.ygeno.2003.11.004
    • Buck MJ, Lieb JD (2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83: 349-360. (Pubitemid 38220840)
    • (2004) Genomics , vol.83 , Issue.3 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 6
    • 0028850043 scopus 로고
    • Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast
    • Freeman K, Gwadz M, Shore D (1995) Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast. Genetics 141: 1253-1262.
    • (1995) Genetics , vol.141 , pp. 1253-1262
    • Freeman, K.1    Gwadz, M.2    Shore, D.3
  • 7
    • 0037478787 scopus 로고    scopus 로고
    • Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms
    • Chou CC, Lin TW, Chen CY, Wang AHJ (2003) Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms. J Bacteriol 185: 4066-4073.
    • (2003) J Bacteriol , vol.185 , pp. 4066-4073
    • Chou, C.C.1    Lin, T.W.2    Chen, C.Y.3    Wang, A.H.J.4
  • 8
    • 80052855771 scopus 로고    scopus 로고
    • iDNA-Prot: Identification of DNA binding proteins using random forest with grey model
    • doi:10.1371/journal.pone.0024756
    • Lin WZ, Fang JA, Xiao X, Chou KC (2011) iDNA-Prot: identification of DNA binding proteins using random forest with grey model. PloS One 6: e24756. doi:10.1371/journal.pone.0024756.
    • (2011) PloS One , vol.6
    • Lin, W.Z.1    Fang, J.A.2    Xiao, X.3    Chou, K.C.4
  • 9
    • 0037470573 scopus 로고    scopus 로고
    • Annotating nucleic acid-binding function based on protein structure
    • DOI 10.1016/S0022-2836(03)00031-7
    • Stawiski EW, Gregoret LM, Mandel-Gutfreund Y (2003) Annotating nucleic acid-binding function based on protein structure. J Mol Biol 326: 1065-1079. (Pubitemid 36263383)
    • (2003) Journal of Molecular Biology , vol.326 , Issue.4 , pp. 1065-1079
    • Stawiski, E.W.1    Gregoret, L.M.2    Mandel-Gutfreund, Y.3
  • 10
    • 4143064791 scopus 로고    scopus 로고
    • Moment-based prediction of DNA-binding proteins
    • DOI 10.1016/j.jmb.2004.05.058, PII S0022283604006382
    • Ahmad S, Sarai A (2004) Moment-based prediction of DNA-binding proteins. J Mol Biol 341: 65-71. doi:10.1016/j.jmb.2004.05.058. (Pubitemid 39090635)
    • (2004) Journal of Molecular Biology , vol.341 , Issue.1 , pp. 65-71
    • Ahmad, S.1    Sarai, A.2
  • 11
    • 47249125424 scopus 로고    scopus 로고
    • DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions
    • DOI 10.1093/nar/gkn332
    • Gao M, Skolnick J (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res 36: 3978-3992. doi:10.1093/nar/gkn332. (Pubitemid 351984814)
    • (2008) Nucleic Acids Research , vol.36 , Issue.12 , pp. 3978-3992
    • Gao, M.1    Skolnick, J.2
  • 12
    • 77955034560 scopus 로고    scopus 로고
    • Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
    • doi:10.1093/bioinformatics/btq295
    • Zhao H, Yang Y, Zhou Y (2010) Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinforma Oxf Engl 26: 1857-1863. doi:10.1093/bioinformatics/ btq295.
    • (2010) Bioinforma Oxf Engl , vol.26 , pp. 1857-1863
    • Zhao, H.1    Yang, Y.2    Zhou, Y.3
  • 13
    • 62649160355 scopus 로고    scopus 로고
    • Identification of DNA-binding proteins using structural, electrostatic and evolutionary features
    • doi:10.1016/j.jmb.2009.02.023
    • Nimrod G, Szilágyi A, Leslie C, Ben-Tal N (2009) Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. J Mol Biol 387: 1040-1053. doi:10.1016/j.jmb.2009.02.023.
    • (2009) J Mol Biol , vol.387 , pp. 1040-1053
    • Nimrod, G.1    Szilágyi, A.2    Leslie, C.3    Ben-Tal, N.4
  • 14
    • 77949596765 scopus 로고    scopus 로고
    • iDBPs: A web server for the identification of DNA binding proteins
    • doi:10.1093/bioinformatics/btq019
    • Nimrod G, Schushan M, Szilágyi A, Leslie C, Ben-Tal N (2010) iDBPs: a web server for the identification of DNA binding proteins. Bioinformatics 26: 692-693. doi:10.1093/bioinformatics/btq019.
    • (2010) Bioinformatics , vol.26 , pp. 692-693
    • Nimrod, G.1    Schushan, M.2    Szilágyi, A.3    Leslie, C.4    Ben-Tal, N.5
  • 15
    • 80054017696 scopus 로고    scopus 로고
    • Prediction of DNA-binding protein based on statistical and geometric features and support vector machines
    • doi:10.1186/1477-5956-9-S1-S1
    • Zhou W, Yan H (2011) Prediction of DNA-binding protein based on statistical and geometric features and support vector machines. Proteome Sci 9 Suppl 1: S1. doi:10.1186/1477-5956-9-S1-S1.
    • (2011) Proteome Sci , vol.9 , Issue.SUPPL. 1
    • Zhou, W.1    Yan, H.2
  • 16
    • 84873900718 scopus 로고    scopus 로고
    • Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search
    • doi:10.1186/1471-2105-13-S10-S3
    • Szabóová A, Kuželka O, Zelezný F, Tolar J (2012) Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search. BMC Bioinformatics 13 Suppl 10: S3. doi:10.1186/1471-2105-13-S10-S3.
    • (2012) BMC Bioinformatics , vol.13 , Issue.SUPPL. 10
    • Szabóová, A.1    Kuželka, O.2    Zelezný, F.3    Tolar, J.4
  • 17
    • 29144504328 scopus 로고    scopus 로고
    • Kernel-based machine learning protocol for predicting DNA-binding proteins
    • DOI 10.1093/nar/gki949
    • Bhardwaj N, Langlois RE, Zhao G, Lu H (2005) Kernel-based machine learning protocol for predicting DNA-binding proteins. Nucleic Acids Res 33: 6486-6493. doi:10.1093/nar/gki949. (Pubitemid 41806412)
    • (2005) Nucleic Acids Research , vol.33 , Issue.20 , pp. 6486-6493
    • Bhardwaj, N.1    Langlois, R.E.2    Zhao, G.3    Lu, H.4
  • 18
    • 33847122913 scopus 로고    scopus 로고
    • Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions
    • DOI 10.1016/j.febslet.2007.01.086, PII S0014579307001263
    • Bhardwaj N, Lu H (2007) Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions. FEBS Lett 581: 1058-1066. doi:10.1016/j.febslet.2007.01.086. (Pubitemid 46282728)
    • (2007) FEBS Letters , vol.581 , Issue.5 , pp. 1058-1066
    • Bhardwaj, N.1    Lu, H.2
  • 19
    • 73449119593 scopus 로고    scopus 로고
    • A threading-based method for the prediction of DNA-binding proteins with application to the human genome
    • doi:10.1371/journal.pcbi.1000567
    • Gao M, Skolnick J (2009) A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS Comput Biol 5: e1000567. doi:10.1371/journal.pcbi.1000567.
    • (2009) PLoS Comput Biol , vol.5
    • Gao, M.1    Skolnick, J.2
  • 20
    • 84874690054 scopus 로고    scopus 로고
    • An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis
    • doi:10.1186/1471-2105-14-90
    • Zou C, Gong J, Li H (2013) An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis. BMC Bioinformatics 14: 90. doi:10.1186/1471-2105-14-90.
    • (2013) BMC Bioinformatics , vol.14 , pp. 90
    • Zou, C.1    Gong, J.2    Li, H.3
  • 21
    • 79951526116 scopus 로고    scopus 로고
    • Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties
    • doi:10.1186/1471-2105-12-S1-S47
    • Huang HL, Lin IC, Liou YF, Tsai CT, Hsu KT, et al. (2011) Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties. BMC Bioinformatics 12 Suppl 1: S47. doi:10.1186/1471-2105-12-S1-S47.
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL. 1
    • Huang, H.L.1    Lin, I.C.2    Liou, Y.F.3    Tsai, C.T.4    Hsu, K.T.5
  • 22
    • 67249090413 scopus 로고    scopus 로고
    • DNA-Prot: Identification of DNA binding proteins from protein sequence information using random forest
    • Kumar KK, Pugalenthi G, Suganthan PN (2009) DNA-Prot: identification of DNA binding proteins from protein sequence information using random forest. J Biomol Struct Dyn 26: 679-686.
    • (2009) J Biomol Struct Dyn , vol.26 , pp. 679-686
    • Kumar, K.K.1    Pugalenthi, G.2    Suganthan, P.N.3
  • 23
    • 38649127567 scopus 로고    scopus 로고
    • Identification of DNA-binding proteins using support vector machines and evolutionary profiles
    • doi:10.1186/1471-2105-8-463
    • Kumar M, Gromiha MM, Raghava GPS (2007) Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinformatics 8: 463. doi:10.1186/1471-2105-8-463.
    • (2007) BMC Bioinformatics , vol.8 , pp. 463
    • Kumar, M.1    Gromiha, M.M.2    Raghava, G.P.S.3
  • 24
    • 33646067733 scopus 로고    scopus 로고
    • Efficient Prediction of Nucleic Acid Binding Function from Low-resolution Protein Structures
    • doi:10.1016/j.jmb.2006.02.053
    • Szilágyi A, Skolnick J (2006) Efficient Prediction of Nucleic Acid Binding Function from Low-resolution Protein Structures. J Mol Biol 358: 922-933. doi:10.1016/j.jmb.2006.02.053.
    • (2006) J Mol Biol , vol.358 , pp. 922-933
    • Szilágyi, A.1    Skolnick, J.2
  • 25
    • 38149007012 scopus 로고    scopus 로고
    • Predicting DNA-binding proteins: Approached from Chou's pseudo amino acid composition and other specific sequence features
    • doi:10.1007/s00726-007-0568-2
    • Fang Y, Guo Y, Feng Y, Li M (2008) Predicting DNA-binding proteins: approached from Chou's pseudo amino acid composition and other specific sequence features. Amino Acids 34: 103-109. doi:10.1007/s00726-007-0568-2.
    • (2008) Amino Acids , vol.34 , pp. 103-109
    • Fang, Y.1    Guo, Y.2    Feng, Y.3    Li, M.4
  • 26
    • 43149115186 scopus 로고    scopus 로고
    • Combing ontologies and dipeptide composition for predicting DNA-binding proteins
    • doi:10.1007/s00726-007-0016-3
    • Nanni L, Lumini A (2008) Combing ontologies and dipeptide composition for predicting DNA-binding proteins. Amino Acids 34: 635-641. doi:10.1007/s00726- 007-0016-3.
    • (2008) Amino Acids , vol.34 , pp. 635-641
    • Nanni, L.1    Lumini, A.2
  • 27
    • 59449107736 scopus 로고    scopus 로고
    • An ensemble of reduced alphabets with protein encoding based on grouped weight for predicting DNA-binding proteins
    • doi:10.1007/s00726-008-0044-7
    • Nanni L, Lumini A (2009) An ensemble of reduced alphabets with protein encoding based on grouped weight for predicting DNA-binding proteins. Amino Acids 36: 167-175. doi:10.1007/s00726-008-0044-7.
    • (2009) Amino Acids , vol.36 , pp. 167-175
    • Nanni, L.1    Lumini, A.2
  • 28
    • 33646510075 scopus 로고    scopus 로고
    • Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines
    • doi:10.1016/j.jtbi.2005.09.018
    • Yu X, Cao J, Cai Y, Shi T, Li Y (2006) Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines. J Theor Biol 240: 175-184. doi:10.1016/j.jtbi.2005.09.018.
    • (2006) J Theor Biol , vol.240 , pp. 175-184
    • Yu, X.1    Cao, J.2    Cai, Y.3    Shi, T.4    Li, Y.5
  • 29
    • 64749100837 scopus 로고    scopus 로고
    • Predicting DNA- and RNA-binding proteins from sequences with kernel methods
    • doi:10.1016/j.jtbi.2009.01.024
    • Shao X, Tian Y, Wu L, Wang Y, Jing L, et al. (2009) Predicting DNA- and RNA-binding proteins from sequences with kernel methods. J Theor Biol 258: 289-293. doi:10.1016/j.jtbi.2009.01.024.
    • (2009) J Theor Biol , vol.258 , pp. 289-293
    • Shao, X.1    Tian, Y.2    Wu, L.3    Wang, Y.4    Jing, L.5
  • 30
    • 0038644483 scopus 로고    scopus 로고
    • Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence
    • DOI 10.1016/S1570-9639(03)00112-2
    • Cai Y, Lin SL (2003) Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence. Biochim Biophys Acta 1648: 127-133. (Pubitemid 38234614)
    • (2003) Biochimica et Biophysica Acta - Proteins and Proteomics , vol.1648 , Issue.1-2 , pp. 127-133
    • Cai, Y.-D.1    Lin, S.L.2
  • 33
    • 79955638463 scopus 로고    scopus 로고
    • Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
    • doi:10.1093/nar/gkq1266
    • Zhao H, Yang Y, Zhou Y (2011) Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res 39: 3017-3025. doi:10.1093/nar/gkq1266.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3017-3025
    • Zhao, H.1    Yang, Y.2    Zhou, Y.3
  • 34
    • 81255197811 scopus 로고    scopus 로고
    • Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction
    • doi:10.4161/rna.8.6.17813
    • Zhao H, Yang Y, Zhou Y (2011) Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. RNA Biol 8: 988-996. doi:10.4161/rna.8.6.17813.
    • (2011) RNA Biol , vol.8 , pp. 988-996
    • Zhao, H.1    Yang, Y.2    Zhou, Y.3
  • 35
    • 50949129815 scopus 로고    scopus 로고
    • Classifying RNA-binding proteins based on electrostatic properties
    • doi:10.1371/journal.pcbi.1000146
    • Shazman S, Mandel-Gutfreund Y (2008) Classifying RNA-binding proteins based on electrostatic properties. PLoS Comput Biol 4: e1000146. doi:10.1371/journal.pcbi.1000146.
    • (2008) PLoS Comput Biol , vol.4
    • Shazman, S.1    Mandel-Gutfreund, Y.2
  • 36
    • 78049479811 scopus 로고    scopus 로고
    • The Text-mining based PubChem Bioassay neighboring analysis
    • doi:10.1186/1471-2105-11-549
    • Han L, Suzek TO, Wang Y, Bryant SH (2010) The Text-mining based PubChem Bioassay neighboring analysis. BMC Bioinformatics 11: 549. doi:10.1186/1471- 2105-11-549.
    • (2010) BMC Bioinformatics , vol.11 , pp. 549
    • Han, L.1    Suzek, T.O.2    Wang, Y.3    Bryant, S.H.4
  • 37
    • 83855162773 scopus 로고    scopus 로고
    • SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles
    • doi:10.1002/jcc.21968
    • Faraggi E, Zhang T, Yang Y, Kurgan L, Zhou Y (2012) SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J Comput Chem 33: 259-267. doi:10.1002/jcc.21968.
    • (2012) J Comput Chem , vol.33 , pp. 259-267
    • Faraggi, E.1    Zhang, T.2    Yang, Y.3    Kurgan, L.4    Zhou, Y.5
  • 39
    • 84860256769 scopus 로고    scopus 로고
    • Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility
    • doi:10.1007/s00726-010-0805-y
    • Zhang H, Zhang T, Gao J, Ruan J, Shen S, et al. (2012) Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility. Amino Acids 42: 271-283. doi:10.1007/s00726-010-0805- y.
    • (2012) Amino Acids , vol.42 , pp. 271-283
    • Zhang, H.1    Zhang, T.2    Gao, J.3    Ruan, J.4    Shen, S.5
  • 40
    • 79251489750 scopus 로고    scopus 로고
    • Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility
    • Zhang T, Zhang H, Chen K, Ruan J, Shen S, et al. (2010) Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility. Curr Protein Pept Sci 11: 609-628.
    • (2010) Curr Protein Pept Sci , vol.11 , pp. 609-628
    • Zhang, T.1    Zhang, H.2    Chen, K.3    Ruan, J.4    Shen, S.5
  • 41
    • 53749083563 scopus 로고    scopus 로고
    • Accurate sequence-based prediction of catalytic residues
    • doi:10.1093/bioinformatics/btn433
    • Zhang T, Zhang H, Chen K, Shen S, Ruan J, et al. (2008) Accurate sequence-based prediction of catalytic residues. Bioinformatics 24: 2329-2338. doi:10.1093/bioinformatics/btn433.
    • (2008) Bioinformatics , vol.24 , pp. 2329-2338
    • Zhang, T.1    Zhang, H.2    Chen, K.3    Shen, S.4    Ruan, J.5
  • 42
    • 0037340834 scopus 로고    scopus 로고
    • Real value prediction of solvent accessibility from amino acid sequence
    • DOI 10.1002/prot.10328
    • Ahmad S, Gromiha MM, Sarai A (2003) Real value prediction of solvent accessibility from amino acid sequence. Proteins 50: 629-635. doi:10.1002/prot.10328. (Pubitemid 36330487)
    • (2003) Proteins: Structure, Function and Genetics , vol.50 , Issue.4 , pp. 629-635
    • Ahmad, S.1    Gromiha, M.M.2    Sarai, A.3
  • 43
    • 84867325297 scopus 로고    scopus 로고
    • Characterization and prediction of the binding site in DNA-binding proteins: Improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters
    • doi:10.1093/nar/gks405
    • Dey S, Pal A, Guharoy M, Sonavane S, 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 Res 40: 7150-7161. doi:10.1093/nar/gks405.
    • (2012) Nucleic Acids Res , vol.40 , pp. 7150-7161
    • Dey, S.1    Pal, A.2    Guharoy, M.3    Sonavane, S.4    Chakrabarti, P.5
  • 44
    • 84860696343 scopus 로고    scopus 로고
    • Protein-RNA interface residue prediction using machine learning: An assessment of the state of the art
    • doi:10.1186/1471-2105-13-89
    • Walia RR, Caragea C, Lewis BA, Towfic FG, Terribilini M, et al. (2012) Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC Bioinformatics 13: 89. doi:10.1186/1471-2105-13-89.
    • (2012) BMC Bioinformatics , vol.13 , pp. 89
    • Walia, R.R.1    Caragea, C.2    Lewis, B.A.3    Towfic, F.G.4    Terribilini, M.5
  • 45
    • 84870415234 scopus 로고    scopus 로고
    • Predicting protein residue-residue contacts using deep networks and boosting
    • doi:10.1093/bioinformatics/bts598
    • Eickholt J, Cheng J (2012) Predicting protein residue-residue contacts using deep networks and boosting. Bioinformatics 28: 3066-3072. doi:10.1093/bioinformatics/bts598.
    • (2012) Bioinformatics , vol.28 , pp. 3066-3072
    • Eickholt, J.1    Cheng, J.2
  • 46
    • 67849110005 scopus 로고    scopus 로고
    • NNcon: Improved protein contact map prediction using 2D-recursive neural networks
    • doi:10.1093/nar/gkp305
    • Tegge AN, Wang Z, Eickholt J, Cheng J (2009) NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res 37: W515-518. doi:10.1093/nar/gkp305.
    • (2009) Nucleic Acids Res , vol.37
    • Tegge, A.N.1    Wang, Z.2    Eickholt, J.3    Cheng, J.4
  • 47
    • 84855184716 scopus 로고    scopus 로고
    • SPINE-D: Accurate prediction of short and long disordered regions by a single neural-network based method
    • Zhang T, Faraggi E, Xue B, Dunker AK, Uversky VN, et al. (2012) SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. J Biomol Struct Dyn 29: 799-813.
    • (2012) J Biomol Struct Dyn , vol.29 , pp. 799-813
    • Zhang, T.1    Faraggi, E.2    Xue, B.3    Dunker, A.K.4    Uversky, V.N.5
  • 48
    • 84862499641 scopus 로고    scopus 로고
    • Prediction of Protein Domain with mRMR Feature Selection and Analysis
    • Available: Accessed 2013 July 10
    • Li BQ, Hu LL, Chen L, Feng KY, Cai YD, et al. (2012) Prediction of Protein Domain with mRMR Feature Selection and Analysis. PLoS ONE 7. Available: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376124/. Accessed 2013 July 10.
    • (2012) PLoS ONE , vol.7
    • Li, B.Q.1    Hu, L.L.2    Chen, L.3    Feng, K.Y.4    Cai, Y.D.5
  • 49
    • 84876136942 scopus 로고    scopus 로고
    • DomHR: Accurately Identifying Domain Boundaries in Proteins Using a Hinge Region Strategy
    • doi:10.1371/journal.pone.0060559
    • Zhang X, Lu L, Song Q, Yang Q, Li D, et al. (2013) DomHR: Accurately Identifying Domain Boundaries in Proteins Using a Hinge Region Strategy. PLoS ONE 8: e60559. doi:10.1371/journal.pone.0060559.
    • (2013) PLoS ONE , vol.8
    • Zhang, X.1    Lu, L.2    Song, Q.3    Yang, Q.4    Li, D.5
  • 50
    • 33748254329 scopus 로고    scopus 로고
    • Predicting G-protein coupled receptors-G-protein coupling specificity based on autocross-covariance transform
    • DOI 10.1002/prot.21097
    • Guo Y, Li M, Lu M, Wen Z, Huang Z (2006) Predicting G-protein coupled receptors-G-protein coupling specificity based on autocross-covariance transform. Proteins 65: 55-60. doi:10.1002/prot.21097. (Pubitemid 44320616)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.1 , pp. 55-60
    • Guo, Y.1    Li, M.2    Lu, M.3    Wen, Z.4    Huang, Z.5
  • 51
    • 70349985248 scopus 로고    scopus 로고
    • A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation
    • doi:10.1093/bioinformatics/btp500
    • Dong Q, Zhou S, Guan J (2009) A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation. Bioinforma Oxf Engl 25: 2655-2662. doi:10.1093/bioinformatics/btp500.
    • (2009) Bioinforma Oxf Engl , vol.25 , pp. 2655-2662
    • Dong, Q.1    Zhou, S.2    Guan, J.3
  • 52
    • 44349159560 scopus 로고    scopus 로고
    • Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
    • DOI 10.1093/nar/gkn159
    • Guo Y, Yu L, Wen Z, Li M (2008) Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucleic Acids Res 36: 3025-3030. doi:10.1093/nar/gkn159. (Pubitemid 351737194)
    • (2008) Nucleic Acids Research , vol.36 , Issue.9 , pp. 3025-3030
    • Guo, Y.1    Yu, L.2    Wen, Z.3    Li, M.4
  • 53
    • 84871787691 scopus 로고    scopus 로고
    • Data mining in the Life Sciences with Random Forest: A walk in the park or lost in the jungle?
    • doi:10.1093/bib/bbs034
    • Touw WG, Bayjanov JR, Overmars L, Backus L, Boekhorst J, et al. (2013) Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? Brief Bioinform 14: 315-326. doi:10.1093/bib/bbs034.
    • (2013) Brief Bioinform , vol.14 , pp. 315-326
    • Touw, W.G.1    Bayjanov, J.R.2    Overmars, L.3    Backus, L.4    Boekhorst, J.5
  • 54
    • 79951527638 scopus 로고    scopus 로고
    • DROP: An SVM domain linker predictor trained with optimal features selected by random forest
    • doi:10.1093/bioinformatics/btq700
    • Ebina T, Toh H, Kuroda Y (2011) DROP: an SVM domain linker predictor trained with optimal features selected by random forest. Bioinforma Oxf Engl 27: 487-494. doi:10.1093/bioinformatics/btq700.
    • (2011) Bioinforma Oxf Engl , vol.27 , pp. 487-494
    • Ebina, T.1    Toh, H.2    Kuroda, Y.3
  • 55
    • 84861813244 scopus 로고    scopus 로고
    • Random forest Gini importance favours SNPs with large minor allele frequency: Impact, sources and recommendations
    • doi:10.1093/bib/bbr053
    • Boulesteix AL, Bender A, Lorenzo Bermejo J, Strobl C (2012) Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations. Brief Bioinform 13: 292-304. doi:10.1093/bib/bbr053.
    • (2012) Brief Bioinform , vol.13 , pp. 292-304
    • Boulesteix, A.L.1    Bender, A.2    Lorenzo Bermejo, J.3    Strobl, C.4
  • 56
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • doi:10.1023/A:1010933404324
    • Breiman L (2001) Random Forests. Mach Learn 45: 5-32. doi:10.1023/A:1010933404324.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 58
    • 0004255908 scopus 로고    scopus 로고
    • 1st edition. New York: McGraw-Hill
    • Mitchell TM (1997) Machine Learning. 1st edition. New York: McGraw-Hill.
    • (1997) Machine Learning
    • Mitchell, T.M.1
  • 59
    • 0037316238 scopus 로고    scopus 로고
    • A naive Bayes model to predict coupling between seven transmembrane domain receptors and G-proteins
    • DOI 10.1093/bioinformatics/19.2.234
    • Cao J, Panetta R, Yue S, Steyaert A, Young-Bellido M, et al. (2003) A naive Bayes model to predict coupling between seven transmembrane domain receptors and G-proteins. Bioinforma Oxf Engl 19: 234-240. (Pubitemid 36181908)
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 234-240
    • Cao, J.1    Panetta, R.2    Yue, S.3    Steyaert, A.4    Young-Bellido, M.5    Ahmad, S.6
  • 60
    • 77955036815 scopus 로고    scopus 로고
    • Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites
    • doi:10.1093/bioinformatics/btq302
    • Murakami Y, Mizuguchi K (2010) Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. Bioinforma Oxf Engl 26: 1841-1848. doi:10.1093/bioinformatics/btq302.
    • (2010) Bioinforma Oxf Engl , vol.26 , pp. 1841-1848
    • Murakami, Y.1    Mizuguchi, K.2
  • 61
    • 84880838767 scopus 로고    scopus 로고
    • Smoothness without Smoothing: Why Gaussian Naive Bayes Is Not Naive for Multi-Subject Searchlight Studies
    • doi:10.1371/journal.pone.0069566
    • Raizada RDS, Lee YS (2013) Smoothness without Smoothing: Why Gaussian Naive Bayes Is Not Naive for Multi-Subject Searchlight Studies. PLoS ONE 8: e69566. doi:10.1371/journal.pone.0069566.
    • (2013) PLoS ONE , vol.8
    • Raizada, R.D.S.1    Lee, Y.S.2
  • 62
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews BW (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 405: 442-451.
    • (1975) Biochim Biophys Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 63
    • 43149103140 scopus 로고    scopus 로고
    • ROC analysis: Applications to the classification of biological sequences and 3D structures
    • DOI 10.1093/bib/bbm064
    • Sonego P, Kocsor A, Pongor S (2008) ROC analysis: applications to the classification of biological sequences and 3D structures. Brief Bioinform 9: 198-209. doi:10.1093/bib/bbm064. (Pubitemid 351637942)
    • (2008) Briefings in Bioinformatics , vol.9 , Issue.3 , pp. 198-209
    • Sonego, P.1    Kocsor, A.2    Pongor, S.3


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