메뉴 건너뛰기




Volumn 4, Issue SUPPL. 1, 2010, Pages

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN; RNA;

EID: 77953886400     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-S1-S3     Document Type: Article
Times cited : (184)

References (20)
  • 1
    • 1542400269 scopus 로고    scopus 로고
    • Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information.
    • 10.1093/bioinformatics/btg432, 14990443
    • Ahmad S, Gromiha MM, Sarai A. Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 2004, 20:477-486. 10.1093/bioinformatics/btg432, 14990443.
    • (2004) Bioinformatics , vol.20 , pp. 477-486
    • Ahmad, S.1    Gromiha, M.M.2    Sarai, A.3
  • 2
    • 33746495377 scopus 로고    scopus 로고
    • Predicting DNA-binding sites of proteins from amino acid sequence.
    • 1534068, 16712732, 10.1186/1471-2105-7-262
    • Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D, Honavar V. Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics 2006, 7:262. 1534068, 16712732, 10.1186/1471-2105-7-262.
    • (2006) BMC Bioinformatics , vol.7 , pp. 262
    • Yan, C.1    Terribilini, M.2    Wu, F.3    Jernigan, R.L.4    Dobbs, D.5    Honavar, V.6
  • 3
    • 33746526551 scopus 로고    scopus 로고
    • Prediction of RNA binding sites in proteins from amino acid sequence.
    • 1524891, 16790841, 10.1261/rna.2197306
    • Terribilini M, Lee JH, Yan C, Jernigan RL, V Honavar V, Dobbs D. Prediction of RNA binding sites in proteins from amino acid sequence. RNA 2006, 12:1450-1462. 1524891, 16790841, 10.1261/rna.2197306.
    • (2006) RNA , vol.12 , pp. 1450-1462
    • Terribilini, M.1    Lee, J.H.2    Yan, C.3    Jernigan, R.L.4    V. Honavar, V.5    Dobbs, D.6
  • 4
    • 33846469006 scopus 로고    scopus 로고
    • Prediction of DNA-binding residues from sequence features.
    • 10.1142/S0219720006002387, 17245807
    • Wang L, Brown SJ. Prediction of DNA-binding residues from sequence features. J Bioinform Comput Biol 2006, 4:1141-1158. 10.1142/S0219720006002387, 17245807.
    • (2006) J Bioinform Comput Biol , vol.4 , pp. 1141-1158
    • Wang, L.1    Brown, S.J.2
  • 5
    • 33747828217 scopus 로고    scopus 로고
    • BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences.
    • 1538853, 16845003, 10.1093/nar/gkl298
    • Wang L, Brown SJ. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res 2006, 34:W243-W248. 1538853, 16845003, 10.1093/nar/gkl298.
    • (2006) Nucleic Acids Res , vol.34
    • Wang, L.1    Brown, S.J.2
  • 6
    • 25444524842 scopus 로고    scopus 로고
    • PSSM-based prediction of DNA binding sites in proteins.
    • 550660, 15720719, 10.1186/1471-2105-6-33
    • Ahmad S, Sarai A. PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics 2005, 6:33. 550660, 15720719, 10.1186/1471-2105-6-33.
    • (2005) BMC Bioinformatics , vol.6 , pp. 33
    • Ahmad, S.1    Sarai, A.2
  • 7
    • 33744817325 scopus 로고    scopus 로고
    • Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins.
    • 10.1002/prot.20977, 16568445
    • Kuznetsov IB, Gou Z, Li R, Hwang S. Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins. Proteins 2006, 64:19-27. 10.1002/prot.20977, 16568445.
    • (2006) Proteins , vol.64 , pp. 19-27
    • Kuznetsov, I.B.1    Gou, Z.2    Li, R.3    Hwang, S.4
  • 8
    • 34047094501 scopus 로고    scopus 로고
    • DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins.
    • 10.1093/bioinformatics/btl672, 17237068
    • Hwang S, Gou Z, Kuznetsov IB. DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics 2007, 23:634-636. 10.1093/bioinformatics/btl672, 17237068.
    • (2007) Bioinformatics , vol.23 , pp. 634-636
    • Hwang, S.1    Gou, Z.2    Kuznetsov, I.B.3
  • 9
    • 1542559402 scopus 로고    scopus 로고
    • Support vector machine applications in computational biology.
    • MIT Press, Scholkopf B, Tsuda K, Vert JP
    • Noble WS. Support vector machine applications in computational biology. Kernel Methods in Computational Biology 2004, MIT Press, Scholkopf B, Tsuda K, Vert JP.
    • (2004) Kernel Methods in Computational Biology
    • Noble, W.S.1
  • 10
  • 12
    • 1842454912 scopus 로고    scopus 로고
    • Prediction of functional sites by analysis of sequence and structure conservation.
    • 2280064, 15010543, 10.1110/ps.03465504
    • Panchenko AR, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci 2004, 13:884-892. 2280064, 15010543, 10.1110/ps.03465504.
    • (2004) Protein Sci , vol.13 , pp. 884-892
    • Panchenko, A.R.1    Kondrashov, F.2    Bryant, S.3
  • 13
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    • 146917, 9254694, 10.1093/nar/25.17.3389
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 146917, 9254694, 10.1093/nar/25.17.3389.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 14
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: an overview.
    • 10.1093/bioinformatics/16.5.412, 10871264
    • Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16:412-424. 10.1093/bioinformatics/16.5.412, 10871264.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.F.4    Nielsen, H.5
  • 15
    • 0023890867 scopus 로고
    • Measuring the accuracy of diagnostic systems.
    • 10.1126/science.3287615, 3287615
    • Swets JA. Measuring the accuracy of diagnostic systems. Science 1988, 240:1285-1293. 10.1126/science.3287615, 3287615.
    • (1988) Science , vol.240 , pp. 1285-1293
    • Swets, J.A.1
  • 16
    • 0031191630 scopus 로고    scopus 로고
    • The use of the area under the ROC curve in the evaluation of machine learning algorithms.
    • Bradley AP. The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recognition 1997, 30:1145-1159.
    • (1997) Pattern Recognition , vol.30 , pp. 1145-1159
    • Bradley, A.P.1
  • 17
    • 0032727991 scopus 로고    scopus 로고
    • Themes in RNA-protein recognition.
    • 10.1006/jmbi.1999.2991, 10550207
    • Draper DE. Themes in RNA-protein recognition. J Mol Biol 1999, 293:255-270. 10.1006/jmbi.1999.2991, 10550207.
    • (1999) J Mol Biol , vol.293 , pp. 255-270
    • Draper, D.E.1
  • 19
    • 0035900649 scopus 로고    scopus 로고
    • Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function.
    • 10.1016/S0092-8674(01)00566-9, 11719189
    • Darnell JC, Jensen KB, Jin P, Brown V, Warren ST, Darnell RB. Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function. Cell 2001, 107:489-499. 10.1016/S0092-8674(01)00566-9, 11719189.
    • (2001) Cell , vol.107 , pp. 489-499
    • Darnell, J.C.1    Jensen, K.B.2    Jin, P.3    Brown, V.4    Warren, S.T.5    Darnell, R.B.6
  • 20
    • 33846665074 scopus 로고    scopus 로고
    • Fragile X related protein 1 isoforms differentially modulate the affinity of fragile X mental retardation protein for G-quartet RNA structure.
    • 1802556, 17170008, 10.1093/nar/gkl1021
    • Bechara E, Davidovic L, Melko M, Bensaid M, Tremblay S, Grosgeorge J, Khandjian EW, Lalli E, Bardoni B. Fragile X related protein 1 isoforms differentially modulate the affinity of fragile X mental retardation protein for G-quartet RNA structure. Nucleic Acids Res 2007, 35:299-306. 1802556, 17170008, 10.1093/nar/gkl1021.
    • (2007) Nucleic Acids Res , vol.35 , pp. 299-306
    • Bechara, E.1    Davidovic, L.2    Melko, M.3    Bensaid, M.4    Tremblay, S.5    Grosgeorge, J.6    Khandjian, E.W.7    Lalli, E.8    Bardoni, B.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.