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Volumn 12, Issue SUPPL. 1, 2011, Pages

Discriminative structural approaches for enzyme active-site prediction

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME REACTION; LOCAL STRUCTURE; MULTIPLE TEMPLATES; PROTEIN SCIENCE; PROTEIN STRUCTURES; STRUCTURAL APPROACH; TEMPLATE ANALYSIS; TEMPLATE-BASED METHOD;

EID: 79951540390     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S1-S49     Document Type: Article
Times cited : (5)

References (24)
  • 1
    • 0003410183 scopus 로고
    • Enzyme Nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
    • New York: Academic Press Inc
    • Webb EC. Enzyme Nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. 1992, New York: Academic Press Inc.
    • (1992)
    • Webb, E.C.1
  • 2
    • 0015505885 scopus 로고
    • Comparison of the active site stereochemistry and substrate conformation in chymotrypsin and subtilisin BPN'
    • 10.1016/0022-2836(72)90391-9, 5064999
    • Wright CS. Comparison of the active site stereochemistry and substrate conformation in chymotrypsin and subtilisin BPN'. J Mol Biol 1972, 67:151-63. 10.1016/0022-2836(72)90391-9, 5064999.
    • (1972) J Mol Biol , vol.67 , pp. 151-163
    • Wright, C.S.1
  • 3
    • 34548241399 scopus 로고    scopus 로고
    • Convergent evolution of enzyme active sites is not a rare phenomenon
    • 10.1016/j.jmb.2007.06.017, 17681532
    • Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ. Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol 2007, 372(3):817-45. 10.1016/j.jmb.2007.06.017, 17681532.
    • (2007) J Mol Biol , vol.372 , Issue.3 , pp. 817-845
    • Gherardini, P.F.1    Wass, M.N.2    Helmer-Citterich, M.3    Sternberg, M.J.4
  • 4
    • 33845658195 scopus 로고    scopus 로고
    • Systematic comparison of catalytic mechanisms of hydrolysis and transfer
    • 10.1002/prot.21193, 17039546
    • Nagano N, Noguchi T, Akiyama Y. Systematic comparison of catalytic mechanisms of hydrolysis and transfer. Proteins 2007, 66:147-59. 10.1002/prot.21193, 17039546.
    • (2007) Proteins , vol.66 , pp. 147-159
    • Nagano, N.1    Noguchi, T.2    Akiyama, Y.3
  • 5
    • 13444302754 scopus 로고    scopus 로고
    • EzCatDB: the Enzyme Catalyticmechanism Database
    • 10.1093/nar/gki080, 540034, 15608227
    • Nagano N. EzCatDB: the Enzyme Catalyticmechanism Database. Nucleic Acids Res 2005, 33(Database issue):D407-12. 10.1093/nar/gki080, 540034, 15608227.
    • (2005) Nucleic Acids Res , vol.33
    • Nagano, N.1
  • 7
    • 0030724039 scopus 로고    scopus 로고
    • TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
    • 10.1002/pro.5560061104, 2143595, 9385633
    • Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997, 6(11):2308-2323. 10.1002/pro.5560061104, 2143595, 9385633.
    • (1997) Protein Sci , vol.6 , Issue.11 , pp. 2308-2323
    • Wallace, A.C.1    Borkakoti, N.2    Thornton, J.M.3
  • 8
    • 0032483312 scopus 로고    scopus 로고
    • Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases
    • 10.1006/jmbi.1998.1993, 9719646
    • Fetrow JS, Skolnick J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J Mol Biol 1998, 281(5):949-68. 10.1006/jmbi.1998.1993, 9719646.
    • (1998) J Mol Biol , vol.281 , Issue.5 , pp. 949-968
    • Fetrow, J.S.1    Skolnick, J.2
  • 9
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • 10.1006/jmbi.1998.2393, 9917419
    • Kleywegt GJ. Recognition of spatial motifs in protein structures. J Mol Biol 1999, 285(4):1887-97. 10.1006/jmbi.1998.2393, 9917419.
    • (1999) J Mol Biol , vol.285 , Issue.4 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 10
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
    • 10.1093/nar/gkg506, 168913, 12824322
    • Stark A, Russell RB. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res 2003, 31(13):3341-4. 10.1093/nar/gkg506, 168913, 12824322.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3341-3344
    • Stark, A.1    Russell, R.B.2
  • 11
    • 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):1644-9. 10.1093/bioinformatics/btg226, 12967960.
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1644-1649
    • Barker, J.A.1    Thornton, J.M.2
  • 12
    • 1442275649 scopus 로고    scopus 로고
    • A novel approach to predict active sites of enzyme molecules
    • 10.1002/prot.10622, 14997541
    • Chou KC, Cai YD. A novel approach to predict active sites of enzyme molecules. Proteins 2004, 55:77-82. 10.1002/prot.10622, 14997541.
    • (2004) Proteins , vol.55 , pp. 77-82
    • Chou, K.C.1    Cai, Y.D.2
  • 13
    • 3242890667 scopus 로고    scopus 로고
    • PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
    • 10.1093/nar/gkh439, 441577, 15215447
    • Ivanisenko VA, Pintus SS, Grigorovich DA, Kolchanov NA. PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res 2004, 32(Web Server issue):W549-54. 10.1093/nar/gkh439, 441577, 15215447.
    • (2004) Nucleic Acids Res , vol.32
    • Ivanisenko, V.A.1    Pintus, S.S.2    Grigorovich, D.A.3    Kolchanov, N.A.4
  • 14
    • 22544486576 scopus 로고    scopus 로고
    • Protein function prediction using local 3D templates
    • 10.1016/j.jmb.2005.05.067, 16019027
    • Laskowski RA, Watson JD, Thornton JM. Protein function prediction using local 3D templates. J Mol Biol 2005, 351(3):614-26. 10.1016/j.jmb.2005.05.067, 16019027.
    • (2005) J Mol Biol , vol.351 , Issue.3 , pp. 614-626
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 15
    • 14744305761 scopus 로고    scopus 로고
    • Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families
    • 10.1016/j.jmb.2005.01.044, 15755451
    • Torrance JW, Bartlett GJ, Porter CT, Thornton JM. Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol 2005, 347(3):565-81. 10.1016/j.jmb.2005.01.044, 15755451.
    • (2005) J Mol Biol , vol.347 , Issue.3 , pp. 565-581
    • Torrance, J.W.1    Bartlett, G.J.2    Porter, C.T.3    Thornton, J.M.4
  • 16
    • 0003684449 scopus 로고    scopus 로고
    • The Elements of Statistical Learning
    • Springer
    • Hastie T, Tibshirani R, Friedman JH. The Elements of Statistical Learning. 2003, Springer.
    • (2003)
    • Hastie, T.1    Tibshirani, R.2    Friedman, J.H.3
  • 17
    • 0037424601 scopus 로고    scopus 로고
    • A model for statistical significance of local similarities in structure
    • 10.1016/S0022-2836(03)00045-7, 12595245
    • Stark A, Sunyaev S, Russell RB. A model for statistical significance of local similarities in structure. J Mol Biol 2003, 326(5):1307-16. 10.1016/S0022-2836(03)00045-7, 12595245.
    • (2003) J Mol Biol , vol.326 , Issue.5 , pp. 1307-1316
    • Stark, A.1    Sunyaev, S.2    Russell, R.B.3
  • 18
    • 0001969211 scopus 로고    scopus 로고
    • Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
    • 10.1016/S0097-8485(96)80004-0, 16718863
    • Gribskov M, Robinson NL. Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput Chem 1996, 20:25-33. 10.1016/S0097-8485(96)80004-0, 16718863.
    • (1996) Comput Chem , vol.20 , pp. 25-33
    • Gribskov, M.1    Robinson, N.L.2
  • 22
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • 10.1006/jmbi.1993.1489, 8377180
    • Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993, 233:123-38. 10.1006/jmbi.1993.1489, 8377180.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 24
    • 84972538798 scopus 로고
    • A Survey of the Statistical Theory of Shape
    • Kendall DG. A Survey of the Statistical Theory of Shape. Statistical Science 1989, 4(2):87-120.
    • (1989) Statistical Science , vol.4 , Issue.2 , pp. 87-120
    • Kendall, D.G.1


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