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Volumn 15, Issue , 2014, Pages

LigandRFs: Random forest ensemble to identify ligand-binding residues from sequence information alone

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION (OF INFORMATION); DECISION TREES; FORECASTING; LIGANDS; PROTEINS;

EID: 84934951264     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (22)

References (38)
  • 1
    • 80855147871 scopus 로고    scopus 로고
    • Assessment of ligandbinding residue predictions in CASP9
    • Schmidt T, Haas J, Gallo Cassarino T, Schwede T: Assessment of ligandbinding residue predictions in CASP9. Proteins 2011, 79(Suppl 10):126-136 [http://dx.doi.org/10.1002/prot.23174].
    • (2011) Proteins , vol.79 , pp. 126-136
    • Schmidt, T.1    Haas, J.2    Gallo Cassarino, T.3    Schwede, T.4
  • 2
    • 34147204158 scopus 로고    scopus 로고
    • NMR structure determination of protein-ligand complexes by lanthanide labeling
    • Pintacuda G, John M, Su XC, Otting G: NMR structure determination of protein-ligand complexes by lanthanide labeling. Acc Chem Res 2007, 40(3):206-212[http://dx.doi.org/10.1021/ar050087z].
    • (2007) Acc Chem Res , vol.40 , Issue.3 , pp. 206-212
    • Pintacuda, G.1    John, M.2    Su, X.C.3    Otting, G.4
  • 3
    • 66349110095 scopus 로고    scopus 로고
    • PICKY: a novel SVDbased NMR spectra peak picking method
    • Alipanahi B, Gao X, Karakoc E, Donaldson L, Li M: PICKY: a novel SVDbased NMR spectra peak picking method. Bioinformatics 2009, 25(12): i268-i275 [http://dx.doi.org/10.1093/bioinformatics/btp225].
    • (2009) Bioinformatics , vol.25 , Issue.12 , pp. i268-i275
    • Alipanahi, B.1    Gao, X.2    Karakoc, E.3    Donaldson, L.4    Li, M.5
  • 4
    • 79952366609 scopus 로고    scopus 로고
    • Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach
    • Ziarek JJ, Peterson FC, Lytle BL, Volkman BF: Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Methods Enzymol 2011, 493:241-275[http://dx.doi.org/10.1016/B978-0-12-381274-2.00010-8].
    • (2011) Methods Enzymol , vol.493 , pp. 241-275
    • Ziarek, J.J.1    Peterson, F.C.2    Lytle, B.L.3    Volkman, B.F.4
  • 5
    • 79952374427 scopus 로고    scopus 로고
    • Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks
    • Jang R, Gao X, Li M: Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks. J Comput Biol 2011, 18(3):347-363 [http://dx.doi.org/10.1089/cmb.2010.0251].
    • (2011) J Comput Biol , vol.18 , Issue.3 , pp. 347-363
    • Jang, R.1    Gao, X.2    Li, M.3
  • 7
    • 84874528183 scopus 로고    scopus 로고
    • Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY
    • Jang R, Gao X, Li M: Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY. BMC Bioinformatics 2012, 13(Suppl 3):S4 [http://dx.doi.org/10.1186/14712105-13-S3-S4].
    • (2012) BMC Bioinformatics , vol.13
    • Jang, R.1    Gao, X.2    Li, M.3
  • 8
    • 84859239922 scopus 로고    scopus 로고
    • WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering
    • Liu Z, Abbas A, Jing BY, Gao X: WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering. Bioinformatics 2012, 28(7):914-920 [http://dx.doi.org/10.1093/bioinformatics/bts078].
    • (2012) Bioinformatics , vol.28 , Issue.7 , pp. 914-920
    • Liu, Z.1    Abbas, A.2    Jing, B.Y.3    Gao, X.4
  • 9
    • 84872010601 scopus 로고    scopus 로고
    • Automatic peak selection by a Benjamini-Hochberg-based algorithm
    • Abbas A, Kong XB, Liu Z, Jing BY, Gao X: Automatic peak selection by a Benjamini-Hochberg-based algorithm. PLoS One 2013, 8:e53112 [http://dx. doi.org/10.1371/journal.pone.0053112].
    • (2013) PLoS One , vol.8
    • Abbas, A.1    Kong, X.B.2    Liu, Z.3    Jing, B.Y.4    Gao, X.5
  • 10
    • 0142153338 scopus 로고    scopus 로고
    • X-ray crystallographic studies of protein-ligand interactions
    • Palmer RA, Niwa H: X-ray crystallographic studies of protein-ligand interactions. Biochem Soc Trans 2003, 31(Pt 5):973-979 [http://dx.doi.org/10.1042/].
    • (2003) Biochem Soc Trans , vol.31 , pp. 973-979
    • Palmer, R.A.1    Niwa, H.2
  • 11
    • 84864328896 scopus 로고    scopus 로고
    • A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information
    • Dai T, Liu Q, Gao J, Cao Z, Zhu R: A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. BMC Bioinformatics 2011, 12(Suppl 14):S9 [http://dx.doi.org/10.1186/1471-2105-12-S14-S9].
    • (2011) BMC Bioinformatics , vol.12
    • Dai, T.1    Liu, Q.2    Gao, J.3    Cao, Z.4    Zhu, R.5
  • 12
    • 79955892164 scopus 로고    scopus 로고
    • FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
    • Roche DB, Tetchner SJ, McGuffin LJ: FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. BMC Bioinformatics 2011, 12:160 [http://dx.doi.org/10.1186/1471-2105-12-160].
    • (2011) BMC Bioinformatics , vol.12 , pp. 160
    • Roche, D.B.1    Tetchner, S.J.2    McGuffin, L.J.3
  • 13
    • 84861485974 scopus 로고    scopus 로고
    • Predicting ligand binding residues and functional sites using multipositional correlations with graph theoretic clustering and kernel CCA
    • Gonzalez AJ, Liao L, Wu CH: Predicting ligand binding residues and functional sites using multipositional correlations with graph theoretic clustering and kernel CCA. IEEE/ACM Trans Comput Biol Bioinform 2012, 9(4):992-1001[http://dx.doi.org/10.1109/TCBB.2011.136].
    • (2012) IEEE/ACM Trans Comput Biol Bioinform , vol.9 , Issue.4 , pp. 992-1001
    • Gonzalez, A.J.1    Liao, L.2    Wu, C.H.3
  • 14
    • 3142747652 scopus 로고    scopus 로고
    • A hint to search for metalloproteins in gene banks
    • Andreini C, Bertini I, Rosato A: A hint to search for metalloproteins in gene banks. Bioinformatics 2004, 20(9):1373-1380 [http://dx.doi.org/10.1093/bioinformatics/bth095].
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1373-1380
    • Andreini, C.1    Bertini, I.2    Rosato, A.3
  • 15
    • 33749036872 scopus 로고    scopus 로고
    • Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks
    • Passerini A, Punta M, Ceroni A, Rost B, Frasconi P: Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 2006, 65(2):305-316 [http://dx.doi.org/10.1002/prot.21135].
    • (2006) Proteins , vol.65 , Issue.2 , pp. 305-316
    • Passerini, A.1    Punta, M.2    Ceroni, A.3    Rost, B.4    Frasconi, P.5
  • 16
    • 40749148150 scopus 로고    scopus 로고
    • Prediction of zinc-binding sites in proteins from sequence
    • Shu N, Zhou T, Hovmöller S: Prediction of zinc-binding sites in proteins from sequence. Bioinformatics 2008, 24(6):775-782 [http://dx.doi.org/10.1093/bioinformatics/btm618].
    • (2008) Bioinformatics , vol.24 , Issue.6 , pp. 775-782
    • Shu, N.1    Zhou, T.2    Hovmöller, S.3
  • 18
    • 75949116562 scopus 로고    scopus 로고
    • LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction
    • Kauffman C, Karypis G: LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction. Bioinformatics 2009, 25(23):3099-3107 [http://dx.doi.org/10.1093/bioinformatics/btp561].
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3099-3107
    • Kauffman, C.1    Karypis, G.2
  • 19
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 20
    • 74249093706 scopus 로고    scopus 로고
    • Assessment of ligand binding residue predictions in CASP8
    • Lopez G, Ezkurdia I, Tress ML: Assessment of ligand binding residue predictions in CASP8. Proteins 2009, 77(Suppl 9):138-146 [http://dx.doi.org/10.1002/prot.22557].
    • (2009) Proteins , vol.77 , pp. 138-146
    • Lopez, G.1    Ezkurdia, I.2    Tress, M.L.3
  • 23
    • 77954893600 scopus 로고    scopus 로고
    • Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information
    • Chen P, Li J: Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information. BMC Bioinformatics 2010, 11:402 [http://dx.doi.org/10.1186/1471-2105-11-402].
    • (2010) BMC Bioinformatics , vol.11 , pp. 402
    • Chen, P.1    Li, J.2
  • 24
    • 84861493822 scopus 로고    scopus 로고
    • Detection of outlier residues for improving interface prediction in protein heterocomplexes
    • Chen P, Wong L, Li J: Detection of outlier residues for improving interface prediction in protein heterocomplexes. IEEE/ACM Trans Comput Biol Bioinform 2012, 9(4):1155-1165 [http://dx.doi.org/10.1109/TCBB.2012.58].
    • (2012) IEEE/ACM Trans Comput Biol Bioinform , vol.9 , Issue.4 , pp. 1155-1165
    • Chen, P.1    Wong, L.2    Li, J.3
  • 25
    • 84880667308 scopus 로고    scopus 로고
    • Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences
    • Chen P, Li J, Wong L, Kuwahara H, Huang JZ, Gao X: Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences. Proteins 2013, 81(8):1351-1362 [http://dx.doi.org/10.1002/prot.24278].
    • (2013) Proteins , vol.81 , Issue.8 , pp. 1351-1362
    • Chen, P.1    Li, J.2    Wong, L.3    Kuwahara, H.4    Huang, J.Z.5    Gao, X.6
  • 26
    • 33846965982 scopus 로고    scopus 로고
    • Prediction of protein B-factors using multi-class bounded SVM
    • Chen P, Wang B, Wong HS, Huang DS: Prediction of protein B-factors using multi-class bounded SVM. Protein Pept Lett 2007, 14(2):185-190.
    • (2007) Protein Pept Lett , vol.14 , Issue.2 , pp. 185-190
    • Chen, P.1    Wang, B.2    Wong, H.S.3    Huang, D.S.4
  • 27
    • 77956938868 scopus 로고    scopus 로고
    • DomSVR: domain boundary prediction with support vector regression from sequence information alone
    • Chen P, Liu C, Burge L, Li J, Mohammad M, Southerland W, Gloster C, Wang B: DomSVR: domain boundary prediction with support vector regression from sequence information alone. Amino Acids 2010, 39(3):713-726 [http://dx.doi.org/10.1007/s00726-010-0506-6].
    • (2010) Amino Acids , vol.39 , Issue.3 , pp. 713-726
    • Chen, P.1    Liu, C.2    Burge, L.3    Li, J.4    Mohammad, M.5    Southerland, W.6    Gloster, C.7    Wang, B.8
  • 28
    • 84866440725 scopus 로고    scopus 로고
    • Protein domain recurrence and order can enhance prediction of protein functions
    • Messih MA, Chitale M, Bajic VB, Kihara D, Gao X: Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics 2012, 28(18):i444-i450 [http://dx.doi.org/10.1093/bioinformatics/bts398].
    • (2012) Bioinformatics , vol.28 , Issue.18 , pp. i444-i450
    • Messih, M.A.1    Chitale, M.2    Bajic, V.B.3    Kihara, D.4    Gao, X.5
  • 29
    • 84862777877 scopus 로고    scopus 로고
    • ProClusEnsem: predicting membrane protein types by fusing different modes of pseudo amino acid composition
    • Wang J, Li Y, Wang Q, You X, Man J, Wang C, Gao X: ProClusEnsem: predicting membrane protein types by fusing different modes of pseudo amino acid composition. Comput Biol Med 2012, 42(5):564-574 [http://dx.doi.org/10.1016/j.compbiomed.2012.01.012].
    • (2012) Comput Biol Med , vol.42 , Issue.5 , pp. 564-574
    • Wang, J.1    Li, Y.2    Wang, Q.3    You, X.4    Man, J.5    Wang, C.6    Gao, X.7
  • 30
    • 84872784072 scopus 로고    scopus 로고
    • ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for proteinprotein comparison in protein database retrieval
    • Wang J, Gao X, Wang Q, Li Y: ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for proteinprotein comparison in protein database retrieval. BMC Bioinformatics 2012, 13(Suppl 7):S2 [http://dx.doi.org/10.1186/1471-2105-13-S7-S2].
    • (2012) BMC Bioinformatics , vol.13
    • Wang, J.1    Gao, X.2    Wang, Q.3    Li, Y.4
  • 31
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L: Random forests. Machine Learning 2001, 45:5-32[http://link.springer.com/article/10.1023%2FA%3A1010933404324].
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 32
    • 67649535959 scopus 로고    scopus 로고
    • Improving consensus contact prediction via server correlation reduction
    • Gao X, Bu D, Xu J, Li M: Improving consensus contact prediction via server correlation reduction. BMC Struct Biol 2009, 9:28 [http://dx.doi.org/10.1186/1472-6807-9-28].
    • (2009) BMC Struct Biol , vol.9 , pp. 28
    • Gao, X.1    Bu, D.2    Xu, J.3    Li, M.4
  • 33
    • 77952597524 scopus 로고    scopus 로고
    • Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers
    • Chen P, Li J: Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers. BMC Struct Biol 2010, 10(Suppl 1):S2 [http://dx.doi.org/10.1186/1472-6807-10-S1-S2].
    • (2010) BMC Struct Biol , vol.10
    • Chen, P.1    Li, J.2
  • 34
    • 78650097203 scopus 로고    scopus 로고
    • Radial basis function neural network ensemble for predicting protein-protein interaction sites in heterocomplexes
    • Wang B, Chen P, Wang P, Zhao G, Zhang X: Radial basis function neural network ensemble for predicting protein-protein interaction sites in heterocomplexes. Protein Pept Lett 2010, 17(9):1111-1116.
    • (2010) Protein Pept Lett , vol.17 , Issue.9 , pp. 1111-1116
    • Wang, B.1    Chen, P.2    Wang, P.3    Zhao, G.4    Zhang, X.5
  • 35
    • 77952825581 scopus 로고    scopus 로고
    • A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
    • Ballester PJ, Mitchell JBO: A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics 2010, 26(9):1169-1175 [http://dx.doi.org/10.1093/bioinformatics/btq112].
    • (2010) Bioinformatics , vol.26 , Issue.9 , pp. 1169-1175
    • Ballester, P.J.1    Mitchell, J.B.O.2
  • 36
    • 80054910093 scopus 로고    scopus 로고
    • Improved prediction of protein ligand-binding sites using random forests
    • Qiu Z, Wang X: Improved prediction of protein ligand-binding sites using random forests. Protein PeptLett 2011, 18(12):1212-1218.
    • (2011) Protein PeptLett , vol.18 , Issue.12 , pp. 1212-1218
    • Qiu, Z.1    Wang, X.2
  • 37
    • 30644470508 scopus 로고    scopus 로고
    • Predicting protein interaction sites from residue spatial sequence profile and evolution rate
    • Wang B, Chen P, Huang DS, Li Jj, Lok TM, Lyu MR: Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett 2006, 580(2):380-384 [http://dx.doi.org/10.1016/j.febslet.2005.11.081].
    • (2006) FEBS Lett , vol.580 , Issue.2 , pp. 380-384
    • Wang, B.1    Chen, P.2    Huang, D.S.3    Li, J.J.4    Lok, T.M.5    Lyu, M.R.6
  • 38
    • 0028922586 scopus 로고
    • LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
    • Wallace AC, Laskowski RA, Thornton JM: LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995, 8(2):127-134.
    • (1995) Protein Eng , vol.8 , Issue.2 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3


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