메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

From sequence to enzyme mechanism using multi-label machine learning

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE; DATABASE SYSTEMS; FORECASTING; PROTEINS; CATALYST ACTIVITY; CLASSIFICATION (OF INFORMATION); ENZYME ACTIVITY; LEARNING SYSTEMS; NEAREST NEIGHBOR SEARCH;

EID: 84902078914     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-150     Document Type: Article
Times cited : (23)

References (58)
  • 5
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    • 308762, 14681376
    • Porter CT, Bartlett GJ, Thornton JM. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004, 32(Database issue):D129-D133. [http://dx.doi.org/10.1093/nar/gkh028], 308762, 14681376.
    • (2004) Nucleic Acids Res , vol.32 , Issue.Database issue
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 7
    • 0042622243 scopus 로고    scopus 로고
    • SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence
    • 10.1093/nar/gkg600, 169006, 12824396
    • Cai CZ, Han LY, Ji ZL, Chen X, Chen YZ. SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res 2003, 31(13):3692-3697. 10.1093/nar/gkg600, 169006, 12824396.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3692-3697
    • Cai, C.Z.1    Han, L.Y.2    Ji, Z.L.3    Chen, X.4    Chen, Y.Z.5
  • 8
    • 1442275650 scopus 로고    scopus 로고
    • Enzyme family classification by support vector machines
    • 10.1002/prot.20045, 14997540
    • Cai CZ, Han LY, Ji ZL, Chen YZ. Enzyme family classification by support vector machines. Proteins 2004, 55:66-76. [http://dx.doi.org/10.1002/prot.20045], 10.1002/prot.20045, 14997540.
    • (2004) Proteins , vol.55 , pp. 66-76
    • Cai, C.Z.1    Han, L.Y.2    Ji, Z.L.3    Chen, Y.Z.4
  • 9
    • 84860154266 scopus 로고    scopus 로고
    • EnzML: Multi-label prediction of enzyme classes using InterPro signatures
    • 10.1186/1471-2105-13-61, 3483700, 22533924
    • De Ferrari L, Aitken S, van Hemert J, Goryanin I. EnzML: Multi-label prediction of enzyme classes using InterPro signatures. BMC Bioinformatics 2012, 13:61. 10.1186/1471-2105-13-61, 3483700, 22533924.
    • (2012) BMC Bioinformatics , vol.13 , pp. 61
    • De Ferrari, L.1    Aitken, S.2    van Hemert, J.3    Goryanin, I.4
  • 10
    • 78650698479 scopus 로고    scopus 로고
    • EMBM - a new enzyme mechanism-based method for rational design of chemical sites of covalent inhibitors
    • 10.1021/ci100330y, 3010454, 21090595
    • Traube T, Vijayakumar S, Hirsch M, Uritsky N, Shokhen M, Albeck A. EMBM - a new enzyme mechanism-based method for rational design of chemical sites of covalent inhibitors. J Chem Inf Model 2010, 50(12):2256-2265. [http://dx.doi.org/10.1021/ci100330y], 10.1021/ci100330y, 3010454, 21090595.
    • (2010) J Chem Inf Model , vol.50 , Issue.12 , pp. 2256-2265
    • Traube, T.1    Vijayakumar, S.2    Hirsch, M.3    Uritsky, N.4    Shokhen, M.5    Albeck, A.6
  • 11
    • 80053373164 scopus 로고    scopus 로고
    • Sequence-based enzyme catalytic domain prediction using clustering and aggregated mutual information content
    • 10.1142/S0219720011005677, 21976378
    • Choi K, Kim S. Sequence-based enzyme catalytic domain prediction using clustering and aggregated mutual information content. J Bioinform Comput Biol 2011, 9(5):597-611. 10.1142/S0219720011005677, 21976378.
    • (2011) J Bioinform Comput Biol , vol.9 , Issue.5 , pp. 597-611
    • Choi, K.1    Kim, S.2
  • 12
    • 34249308113 scopus 로고    scopus 로고
    • Livesay DR: How accurate and statistically robust are catalytic site predictions based on closeness centrality?
    • 10.1186/1471-2105-8-153, 1876251, 17498304
    • Chea E. Livesay DR: How accurate and statistically robust are catalytic site predictions based on closeness centrality?. BMC Bioinformatics 2007, 8:153. [http://dx.doi.org/10.1186/1471-2105-8-153], 10.1186/1471-2105-8-153, 1876251, 17498304.
    • (2007) BMC Bioinformatics , vol.8 , pp. 153
    • Chea, E.1
  • 13
    • 35348873256 scopus 로고    scopus 로고
    • Predicting active site residue annotations in the Pfam database
    • 10.1186/1471-2105-8-298, 2025603, 17688688
    • Mistry J, Bateman A, Finn RD. Predicting active site residue annotations in the Pfam database. BMC Bioinformatics 2007, 8:298. [http://dx.doi.org/10.1186/1471-2105-8-298], 10.1186/1471-2105-8-298, 2025603, 17688688.
    • (2007) BMC Bioinformatics , vol.8 , pp. 298
    • Mistry, J.1    Bateman, A.2    Finn, R.D.3
  • 14
    • 13444302754 scopus 로고    scopus 로고
    • EzCatDB: the enzyme catalytic-mechanism database
    • 540034, 15608227
    • Nagano N. EzCatDB: the enzyme catalytic-mechanism database. Nucleic Acids Res 2005, 33(Database issue):D407-D412. [http://dx.doi.org/10.1093/nar/gki080], 540034, 15608227.
    • (2005) Nucleic Acids Res , vol.33 , Issue.Database issue
    • Nagano, N.1
  • 15
    • 43349084847 scopus 로고    scopus 로고
    • Using the structure-function linkage database to characterize functional domains in enzymes
    • Unit 2.10 Chapter 2
    • Brown S, Babbitt P. Using the structure-function linkage database to characterize functional domains in enzymes. Curr Protoc Bioinformatics 2006, Chapter 2:Unit 2.10. [http://dx.doi.org/10.1002/0471250953.bi0210s13].
    • (2006) Curr Protoc Bioinformatics
    • Brown, S.1    Babbitt, P.2
  • 16
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the universal protein resource (UniProt) in 2013
    • 3531094, 23161681
    • Consortium U. Update on activities at the universal protein resource (UniProt) in 2013. Nucleic Acids Res 2013, 41(Database issue):D43-D47. 3531094, 23161681.
    • (2013) Nucleic Acids Res , vol.41 , Issue.Database issue
    • Consortium, U.1
  • 19
    • 36549003965 scopus 로고    scopus 로고
    • InterPro and InterProScan: tools for protein sequence classification and comparison
    • 10.1007/978-1-59745-515-2_5, 18025686
    • Mulder N, Apweiler R. InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol 2007, 396:59-70. 10.1007/978-1-59745-515-2_5, 18025686.
    • (2007) Methods Mol Biol , vol.396 , pp. 59-70
    • Mulder, N.1    Apweiler, R.2
  • 22
    • 84874969184 scopus 로고    scopus 로고
    • PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
    • 3531194, 23193289
    • Mi H, Muruganujan A, Thomas PD. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 2013, 41(Database issue):D377-D386. [http://dx.doi.org/10.1093/nar/gks1118], 3531194, 23193289.
    • (2013) Nucleic Acids Res , vol.41 , Issue.Database issue
    • Mi, H.1    Muruganujan, A.2    Thomas, P.D.3
  • 26
    • 13444305296 scopus 로고    scopus 로고
    • The ProDom database of protein domain families: more emphasis on 3D
    • 539988, 15608179
    • Bru C, Courcelle E, CarrÃĺre S, Beausse Y, Dalmar S, Kahn D. The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res 2005, 33(Database issue):D212-D215. [http://dx.doi.org/10.1093/nar/gki034], 539988, 15608179.
    • (2005) Nucleic Acids Res , vol.33 , Issue.Database issue
    • Bru, C.1    Courcelle, E.2    CarrÃĺre, S.3    Beausse, Y.4    Dalmar, S.5    Kahn, D.6
  • 28
    • 84862221167 scopus 로고    scopus 로고
    • SMART 7: recent updates to the protein domain annotation resource
    • 3245027, 22053084
    • Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 2012, 40(Database issue):D302-D305. [http://dx.doi.org/10.1093/nar/gkr931], 3245027, 22053084.
    • (2012) Nucleic Acids Res , vol.40 , Issue.Database issue
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 29
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • 10.1006/jmbi.2001.5080, 11697912
    • Gough J, Karplus K, Hughey R, Chothia C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001, 313(4):903-919. [http://dx.doi.org/10.1006/jmbi.2001.5080], 10.1006/jmbi.2001.5080, 11697912.
    • (2001) J Mol Biol , vol.313 , Issue.4 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 30
  • 31
    • 84891800735 scopus 로고    scopus 로고
    • The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes
    • 3964973, 24319146
    • Furnham N, Holliday GL, de Beer TAP, Jacobsen JOB, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res 2014, 42(Database issue):D485-D489. [http://dx.doi.org/10.1093/nar/gkt1243], 3964973, 24319146.
    • (2014) Nucleic Acids Res , vol.42 , Issue.Database issue
    • Furnham, N.1    Holliday, G.L.2    de Beer, T.A.P.3    Jacobsen, J.O.B.4    Pearson, W.R.5    Thornton, J.M.6
  • 32
    • 0141850386 scopus 로고    scopus 로고
    • An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis
    • 10.1093/bioinformatics/btg226, 12967960
    • Barker JA, Thornton JM. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 2003, 19(13):1644-1649. 10.1093/bioinformatics/btg226, 12967960.
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1644-1649
    • Barker, J.A.1    Thornton, J.M.2
  • 33
    • 22544441094 scopus 로고    scopus 로고
    • ProFunc: a server for predicting protein function from 3D structure
    • 1160175, 15980588
    • Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005, 33(Web Server issue):W89-W93. [http://dx.doi.org/10.1093/nar/gki414], 1160175, 15980588.
    • (2005) Nucleic Acids Res , vol.33 , Issue.Web Server issue
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 34
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: the European molecular biology open software suite
    • 10.1016/S0168-9525(00)02024-2, 10827456
    • Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
    • (2000) Trends Genet , vol.16 , Issue.6 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 35
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • 10.1016/0022-2836(70)90057-4, 5420325
    • Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48(3):443-453. [http://www.sciencedirect.com/science/article/pii/0022283670900574], 10.1016/0022-2836(70)90057-4, 5420325.
    • (1970) J Mol Biol , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 36
    • 0025725905 scopus 로고
    • Instance-based learning algorithms
    • Aha D, Kibler D. Instance-based learning algorithms. Mach Learn 1991, 6:37-66.
    • (1991) Mach Learn , vol.6 , pp. 37-66
    • Aha, D.1    Kibler, D.2
  • 37
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • Breiman L. Random Forests. Mach Learn 2001, 45:5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 40
    • 0027580356 scopus 로고
    • Very simple classification rules perform well on most commonly used datasets
    • Holte RC. Very simple classification rules perform well on most commonly used datasets. Mach Learn 1993, 11:63-90.
    • (1993) Mach Learn , vol.11 , pp. 63-90
    • Holte, R.C.1
  • 42
    • 0000545946 scopus 로고    scopus 로고
    • Improvements to Platt's SMO Algorithm for SVM classifier design
    • Keerthi SS, Shevade SK, Bhattacharyya C, Murthy KRK. Improvements to Platt's SMO Algorithm for SVM classifier design. Neural Comput 2001, 13(3):637-649. [http://dx.doi.org/10.1162/089976601300014493].
    • (2001) Neural Comput , vol.13 , Issue.3 , pp. 637-649
    • Keerthi, S.S.1    Shevade, S.K.2    Bhattacharyya, C.3    Murthy, K.R.K.4
  • 43
    • 0003120218 scopus 로고    scopus 로고
    • Fast training of support vector machines using sequential minimal optimization
    • Cambridge, Massachusetts: MIT Press
    • Platt J. Fast training of support vector machines using sequential minimal optimization. Advances in Kernel Methods - Support Vector Learning. Edited by Schoelkopf B, Burges C, Smola A 1998, Cambridge, Massachusetts: MIT Press, [http://research.microsoft.com/en-us/um/people/jplatt/smo-book.pdf].
    • (1998) Advances in Kernel Methods - Support Vector Learning. Edited by Schoelkopf B, Burges C, Smola A
    • Platt, J.1
  • 49
    • 52949089060 scopus 로고    scopus 로고
    • Random k -Labelsets: an ensemble method for multilabel classification
    • Tsoumakas G, Vlahavas I. Random k -Labelsets: an ensemble method for multilabel classification. 2007, [http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.97.5044&rep=rep1&type=pdf].
    • (2007)
    • Tsoumakas, G.1    Vlahavas, I.2
  • 51
    • 33748366796 scopus 로고    scopus 로고
    • Multilabel neural networks with applications to functional genomics and text categorization
    • Zhang ML, Zhou ZH. Multilabel neural networks with applications to functional genomics and text categorization. Knowl Data Eng IEEE Trans on 2006, 18(10):1338-1351.
    • (2006) Knowl Data Eng IEEE Trans on , vol.18 , Issue.10 , pp. 1338-1351
    • Zhang, M.L.1    Zhou, Z.H.2
  • 52
    • 84980090975 scopus 로고
    • The distribution of the flora in the alpine zone 1
    • Jaccard P. The distribution of the flora in the alpine zone 1. New Phytologist 1912, 11(2):37-50. [http://dx.doi.org/10.1111/j.1469-8137.1912.tb05611.x].
    • (1912) New Phytologist , vol.11 , Issue.2 , pp. 37-50
    • Jaccard, P.1
  • 54
    • 65649138430 scopus 로고    scopus 로고
    • A systematic analysis of performance measures for classification tasks
    • Sokolova M, Lapalme G. A systematic analysis of performance measures for classification tasks. Inf Process Manag 2009, 45(4):427-437. [http://www.sciencedirect.com/science/article/pii/S0306457309000259].
    • (2009) Inf Process Manag , vol.45 , Issue.4 , pp. 427-437
    • Sokolova, M.1    Lapalme, G.2
  • 55
    • 0022833822 scopus 로고
    • Primary structures of canine pancreatic lipase and phospholipase A2 messenger RNAs
    • 10.1097/00006676-198609000-00007, 3562437
    • Kerfelec B, LaForge KS, Puigserver A, Scheele G. Primary structures of canine pancreatic lipase and phospholipase A2 messenger RNAs. Pancreas 1986, 1(5):430-437. 10.1097/00006676-198609000-00007, 3562437.
    • (1986) Pancreas , vol.1 , Issue.5 , pp. 430-437
    • Kerfelec, B.1    LaForge, K.S.2    Puigserver, A.3    Scheele, G.4
  • 57
    • 0031873787 scopus 로고    scopus 로고
    • Reactivation of the totally inactive pancreatic lipase RP1 by structure-predicted point mutations
    • 10.1002/(SICI)1097-0134(19980901)32:4<523::AID-PROT10>3.0.CO;2-E, 9726421
    • Roussel A, de Caro J, Bezzine S, Gastinel L, de Caro A, Carrière F, Leydier S, Verger R, Cambillau C. Reactivation of the totally inactive pancreatic lipase RP1 by structure-predicted point mutations. Proteins 1998, 32(4):523-531. 10.1002/(SICI)1097-0134(19980901)32:4<523::AID-PROT10>3.0.CO;2-E, 9726421.
    • (1998) Proteins , vol.32 , Issue.4 , pp. 523-531
    • Roussel, A.1    de Caro, J.2    Bezzine, S.3    Gastinel, L.4    de Caro, A.5    Carrière, F.6    Leydier, S.7    Verger, R.8    Cambillau, C.9
  • 58
    • 1542714925 scopus 로고    scopus 로고
    • Mismatch string kernels for discriminative protein classification
    • 10.1093/bioinformatics/btg431, 14990442
    • Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. Mismatch string kernels for discriminative protein classification. Bioinformatics 2004, 20(4):467-476. [http://bioinformatics.oxfordjournals.org/content/20/4/467.abstract], 10.1093/bioinformatics/btg431, 14990442.
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 467-476
    • Leslie, C.S.1    Eskin, E.2    Cohen, A.3    Weston, J.4    Noble, W.S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.