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Volumn 10, Issue , 2009, Pages

Enzyme classification with peptide programs: A comparative study

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE PREDICTION; CORRELATION COEFFICIENT; ENZYME CLASSIFICATION; MACHINE LEARNING METHODS; PROPAGATION OF ERROR; PROTEIN CLASSIFICATION; SEQUENCE ALIGNMENTS; SUPPORT VECTOR MACHINE (SVMS);

EID: 68949098339     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-231     Document Type: Article
Times cited : (6)

References (31)
  • 2
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • 10944397
    • Devos D Valencia A Practical limits of function prediction Proteins 2000, 41:98-107 10944397
    • (2000) Proteins , vol.41 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 3
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • 14568541
    • Tian W Skolnick J How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol 2003, 333:863-882 14568541
    • (2003) J Mol Biol , vol.333 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 4
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • 11485799
    • Devos D Valencia A Intrinsic errors in genome annotation Trends Genet 2001, 17(8):429-431 11485799
    • (2001) Trends Genet , vol.17 , Issue.8 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 5
    • 34250790725 scopus 로고    scopus 로고
    • Estimating the annotation error rate of curated GO database sequence annotations
    • 1892569 17519041
    • Jones CE Brown AL Baumann U Estimating the annotation error rate of curated GO database sequence annotations BMC Bioinformatics 2007, 8:170 1892569 17519041
    • (2007) BMC Bioinformatics , vol.8 , pp. 170
    • Jones, C.E.1    Brown, A.L.2    Baumann, U.3
  • 6
    • 33750125547 scopus 로고    scopus 로고
    • Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity
    • 16791826
    • Han L Cui J Lin H Ji Z Cao Z Li Y Chen Y Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity Proteomics 2006, 6:4023-4037 16791826
    • (2006) Proteomics , vol.6 , pp. 4023-4037
    • Han, L.1    Cui, J.2    Lin, H.3    Ji, Z.4    Cao, Z.5    Li, Y.6    Chen, Y.7
  • 7
    • 34249666548 scopus 로고    scopus 로고
    • Learning to translate sequence and structure to function: Identifying DNA binding and membrane binding proteins
    • 2706547 17436108
    • Langlois RE Carson MB Bhardwaj N Lu H Learning to translate sequence and structure to function: Identifying DNA binding and membrane binding proteins Ann Biomed Eng 2007, 35:1043-1052 2706547 17436108
    • (2007) Ann Biomed Eng , vol.35 , pp. 1043-1052
    • Langlois, R.E.1    Carson, M.B.2    Bhardwaj, N.3    Lu, H.4
  • 8
    • 33845524104 scopus 로고    scopus 로고
    • Classification of proteins multiple-labelled and single-labelled with protein functional classes
    • Yang MQ Yang JY Ersoy OK Classification of proteins multiple-labelled and single-labelled with protein functional classes Int J Gen Syst 2007, 36:91-109
    • (2007) Int J Gen Syst , vol.36 , pp. 91-109
    • Yang, M.Q.1    Yang, J.Y.2    Ersoy, O.K.3
  • 9
    • 0035882573 scopus 로고    scopus 로고
    • PRED-CLASS: Cascading Neural networks for generalized protein classification and genome wide applications
    • 11455609
    • Pasquier C Promponas V Hamodrakas SJ PRED-CLASS: Cascading Neural networks for generalized protein classification and genome wide applications Proteins 2001, 44:361-369 11455609
    • (2001) Proteins , vol.44 , pp. 361-369
    • Pasquier, C.1    Promponas, V.2    Hamodrakas, S.J.3
  • 10
    • 34249857996 scopus 로고    scopus 로고
    • Bio-basis function neural networks in protein data mining
    • Yang ZR Hamer R Bio-basis function neural networks in protein data mining Curr Pharm Design 2007, 13:1403-1413
    • (2007) Curr Pharm Design , vol.13 , pp. 1403-1413
    • Yang, Z.R.1    Hamer, R.2
  • 11
    • 29144504328 scopus 로고    scopus 로고
    • Kernel-based machine learning protocol for predicting DNA-binding proteins
    • 1283538 16284202
    • Bhardwaj N Langlois RE Zhao GJ Lu H Kernel-based machine learning protocol for predicting DNA-binding proteins Nucleic Acids Res 2005, 33:6486-6493 1283538 16284202
    • (2005) Nucleic Acids Res , vol.33 , pp. 6486-6493
    • Bhardwaj, N.1    Langlois, R.E.2    Zhao, G.J.3    Lu, H.4
  • 12
    • 34147121960 scopus 로고    scopus 로고
    • Predicting protein function by machine learning on amino acid sequences - A critical evaluation
    • 1847686 17374164
    • Al-Shahib A Breitling R Gilbert DR Predicting protein function by machine learning on amino acid sequences - a critical evaluation BMC Genomics 2007, 8:78 1847686 17374164
    • (2007) BMC Genomics , vol.8 , pp. 78
    • Al-Shahib, A.1    Breitling, R.2    Gilbert, D.R.3
  • 13
    • 1442275650 scopus 로고    scopus 로고
    • Enzyme family classification by support vector machines
    • 14997540
    • Cai CZ Han LY Ji ZL Chen YZ Enzyme family classification by support vector machines Proteins 2004, 55:66-76 14997540
    • (2004) Proteins , vol.55 , pp. 66-76
    • Cai, C.Z.1    Han, L.Y.2    Ji, Z.L.3    Chen, Y.Z.4
  • 14
    • 39849091628 scopus 로고    scopus 로고
    • VirulentPred: A SVM based prediction method for virulent proteins in bacterial pathogens
    • 2254373 18226234
    • Garg A Gupta D VirulentPred: A SVM based prediction method for virulent proteins in bacterial pathogens BMC Bioinformatics 2008, 9:62 2254373 18226234
    • (2008) BMC Bioinformatics , vol.9 , pp. 62
    • Garg, A.1    Gupta, D.2
  • 15
    • 13444251475 scopus 로고    scopus 로고
    • Predicting functional family of novel enzymes irrespective of sequence similarity: A statistical learning approach
    • 535691 15585667
    • Han LY Cai CZ Ji ZL Cao ZW Cui J Chen YZ Predicting functional family of novel enzymes irrespective of sequence similarity: A statistical learning approach Nucleic Acids Res 2004, 32(21):6437-6444 535691 15585667
    • (2004) Nucleic Acids Res , vol.32 , Issue.21 , pp. 6437-6444
    • Han, L.Y.1    Cai, C.Z.2    Ji, Z.L.3    Cao, Z.W.4    Cui, J.5    Chen, Y.Z.6
  • 16
    • 38649127567 scopus 로고    scopus 로고
    • Identification of DNA-binding proteins using support vector machines and evolutionary profiles
    • 2216048 18042272
    • Kumar M Gromiha MM Raghava GPS Identification of DNA-binding proteins using support vector machines and evolutionary profiles BMC Bioinformatics 2007, 8:463 2216048 18042272
    • (2007) BMC Bioinformatics , vol.8 , pp. 463
    • Kumar, M.1    Gromiha, M.M.2    Raghava, G.P.S.3
  • 17
    • 33750975917 scopus 로고    scopus 로고
    • Support vector machine learning from heterogeneous data: An empirical analysis using protein sequence and structure
    • 16966363
    • Lewis DP Jebara T Noble WS Support vector machine learning from heterogeneous data: An empirical analysis using protein sequence and structure Bioinformatics 2006, 22:2753-2760 16966363
    • (2006) Bioinformatics , vol.22 , pp. 2753-2760
    • Lewis, D.P.1    Jebara, T.2    Noble, W.S.3
  • 18
    • 33947407691 scopus 로고    scopus 로고
    • Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach
    • 1764469 17254297
    • Lin HH Han LY Zhang HL Zheng CZ Xie B Cao ZW Chen YZ Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach BMC Bioinformatics 2006, 7(Suppl 5):S13 1764469 17254297
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 5
    • Lin, H.H.1    Han, L.Y.2    Zhang, H.L.3    Zheng, C.Z.4    Xie, B.5    Cao, Z.W.6    Chen, Y.Z.7
  • 19
    • 39549116279 scopus 로고    scopus 로고
    • A genetic approach for building different alphabets for peptide and protein classification
    • 2246158 18218100
    • Nanni L Lumini A A genetic approach for building different alphabets for peptide and protein classification BMC Bioinformatics 2008, 9:45 2246158 18218100
    • (2008) BMC Bioinformatics , vol.9 , pp. 45
    • Nanni, L.1    Lumini, A.2
  • 20
    • 33846069758 scopus 로고    scopus 로고
    • Ensemblator: An ensemble of classifiers for reliable classification of Biological Data
    • Nanni L Lumini A Ensemblator: An ensemble of classifiers for reliable classification of Biological Data Pattern Recognit Letters 2007, 28:622-630
    • (2007) Pattern Recognit Letters , vol.28 , pp. 622-630
    • Nanni, L.1    Lumini, A.2
  • 21
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of Protein Cellular Attributes Using Pseudo-Amino Acid Composition
    • 11288174
    • Chou K Prediction of Protein Cellular Attributes Using Pseudo-Amino Acid Composition Proteins 2001, 43:246-255 11288174
    • (2001) Proteins , vol.43 , pp. 246-255
    • Chou, K.1
  • 22
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequence
    • 41034 7568000
    • Dubchak I Muchnik I Holbrook SR Kim S Prediction of protein folding class using global description of amino acid sequence Proc Natl Acad Sci 1995, 92:8700-8704 41034 7568000
    • (1995) Proc Natl Acad Sci , vol.92 , pp. 8700-8704
    • Dubchak, I.1    Muchnik, I.2    Holbrook, S.R.3    Kim, S.4
  • 23
    • 33747816816 scopus 로고    scopus 로고
    • PROFEAT: A web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
    • Web Server 1538821 16845018
    • Li ZR Lin HH Han LY Jiang L Chen X Chen YZ PROFEAT: A web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence Nucleic Acid Res 2006, 34: Web Server W32-37 1538821 16845018
    • (2006) Nucleic Acid Res , vol.34
    • Li, Z.R.1    Lin, H.H.2    Han, L.Y.3    Jiang, L.4    Chen, X.5    Chen, Y.Z.6
  • 24
    • 34948861260 scopus 로고    scopus 로고
    • Efficacy of different protein descriptors in predicting protein functional families
    • 1997217 17705863
    • Ong SAK Lin HH Chen YZ Li ZR Cao Z Efficacy of different protein descriptors in predicting protein functional families BMC Bioinformatics 2007, 8:300 1997217 17705863
    • (2007) BMC Bioinformatics , vol.8 , pp. 300
    • Ong, S.A.K.1    Lin, H.H.2    Chen, Y.Z.3    Li, Z.R.4    Cao, Z.5
  • 26
    • 0037403516 scopus 로고    scopus 로고
    • Measures of Diversity in Classifier Ensembles and Their Relationship with the Ensemble Accuracy
    • Kuncheva LI Whitaker CJ Measures of Diversity in Classifier Ensembles and Their Relationship with the Ensemble Accuracy Machine Learning 2003, 51:181-207
    • (2003) Machine Learning , vol.51 , pp. 181-207
    • Kuncheva, L.I.1    Whitaker, C.J.2
  • 27
    • 0030211964 scopus 로고    scopus 로고
    • Bagging predictors
    • Breiman L Bagging predictors Machine Learning 1996, 24(2):123-140
    • (1996) Machine Learning , vol.24 , Issue.2 , pp. 123-140
    • Breiman, L.1
  • 28
    • 65349193478 scopus 로고    scopus 로고
    • Protein classification combining surface analysis and primary structure
    • 19188137
    • Nanni L Mazzara S Pattini L Lumini A Protein classification combining surface analysis and primary structure Protein Eng Des Sel 2009, 22:267-272 19188137
    • (2009) Protein Eng Des Sel , vol.22 , pp. 267-272
    • Nanni, L.1    Mazzara, S.2    Pattini, L.3    Lumini, A.4
  • 29
    • 0033963089 scopus 로고    scopus 로고
    • The ENZYME database in 2000
    • 102465 10592255
    • Bairoch A The ENZYME database in 2000 Nucleic Acids Res 2000, 28:304-305 102465 10592255
    • (2000) Nucleic Acids Res , vol.28 , pp. 304-305
    • Bairoch, A.1
  • 30
    • 26444479778 scopus 로고
    • Optimisation by Simulated Annealing
    • 17813860
    • Kirkpatrick S Gelatt CD Vecchi MP Optimisation by Simulated Annealing Science 1983, 220(4598):671-680 17813860
    • (1983) Science , vol.220 , Issue.4598 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3


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