메뉴 건너뛰기




Volumn 10, Issue SUPPL. 1, 2009, Pages

Prediction of DNA-binding residues from protein sequence information using random forests

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CLASSIFIER; CONTROLLED STUDY; DNA BINDING MOTIF; INFORMATION PROCESSING; MOLECULAR EVOLUTION; PROTEIN DATABASE; PROTEIN DNA BINDING; RANDOM FOREST; STRUCTURE ANALYSIS; ALGORITHM; ARTIFICIAL INTELLIGENCE; BINDING SITE; BIOLOGY; COMPUTER PROGRAM; METABOLISM; METHODOLOGY; ROC CURVE; SEQUENCE ANALYSIS;

EID: 67650539034     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-S1-S1     Document Type: Article
Times cited : (100)

References (17)
  • 1
    • 20444382737 scopus 로고    scopus 로고
    • Regulation of transcription: From lambda to eukaryotes
    • 10.1016/j.tibs.2005.04.003 15950866
    • Ptashne M Regulation of transcription: From lambda to eukaryotes Trends Biochem Sci 2005, 30:275-279. 10.1016/j.tibs.2005.04.003 15950866
    • (2005) Trends Biochem Sci , vol.30 , pp. 275-279
    • Ptashne, M.1
  • 3
    • 20544460658 scopus 로고    scopus 로고
    • Protein-DNA recognition patterns and predictions
    • 10.1146/annurev.biophys.34.040204.144537 15869395
    • Sarai A Kono H Protein-DNA recognition patterns and predictions Annu Rev Biophys Biomol Struct 2005, 34:379-398. 10.1146/ annurev.biophys.34.040204.144537 15869395
    • (2005) Annu Rev Biophys Biomol Struct , vol.34 , pp. 379-398
    • Sarai, A.1    Kono, H.2
  • 4
    • 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
  • 5
    • 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
  • 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
    • 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
  • 10
    • 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
  • 11
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • 10.1023/A:1010933404324
    • Breiman L Random forests Machine Learning 2001, 45:5-32. 10.1023/ A:1010933404324
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 13
    • 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
  • 14
    • 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
  • 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. 10.1016/S0031-3203(96)00142-2
    • (1997) Pattern Recognition , vol.30 , pp. 1145-1159
    • Bradley, A.P.1
  • 17
    • 0036500260 scopus 로고    scopus 로고
    • Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR
    • 125875 11867549 10.1093/emboj/21.5.1210
    • Schumacher MA Miller MC Grkovic S Brown MH Skurray RA Brennan RG Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR EMBO J 2002, 21:1210-1218. 125875 11867549 10.1093/emboj/21.5.1210
    • (2002) EMBO J , vol.21 , pp. 1210-1218
    • Schumacher, M.A.1    Miller, M.C.2    Grkovic, S.3    Brown, M.H.4    Skurray, R.A.5    Brennan, R.G.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.