메뉴 건너뛰기




Volumn 7, Issue 10, 2012, Pages

Accurate Prediction of Protein Catalytic Residues by Side Chain Orientation and Residue Contact Density

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84868143151     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047951     Document Type: Article
Times cited : (15)

References (28)
  • 1
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • Capra JA, Singh M, (2007) Predicting functionally important residues from sequence conservation. Bioinformatics 23: 1875-1882.
    • (2007) Bioinformatics , vol.23 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 2
    • 11344278220 scopus 로고    scopus 로고
    • Predicting protein functional sites with phylogenetic motifs
    • La D, Sutch B, Livesay DR, (2005) Predicting protein functional sites with phylogenetic motifs. Proteins 58: 309-320.
    • (2005) Proteins , vol.58 , pp. 309-320
    • La, D.1    Sutch, B.2    Livesay, D.R.3
  • 3
    • 0344405703 scopus 로고    scopus 로고
    • Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation
    • Ota M, Kinoshita K, Nishikawa K, (2003) Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. Journal of Molecular Biology 327: 1053-1064.
    • (2003) Journal of Molecular Biology , vol.327 , pp. 1053-1064
    • Ota, M.1    Kinoshita, K.2    Nishikawa, K.3
  • 5
    • 14744305761 scopus 로고    scopus 로고
    • Using a Library of Structural Templates to Recognise Catalytic Sites and Explore their Evolution in Homologous Families
    • Torrance JW, Bartlett GJ, Porter CT, Thornton JM, (2005) Using a Library of Structural Templates to Recognise Catalytic Sites and Explore their Evolution in Homologous Families. Journal of Molecular Biology 347: 565-581.
    • (2005) Journal of Molecular Biology , vol.347 , pp. 565-581
    • Torrance, J.W.1    Bartlett, G.J.2    Porter, C.T.3    Thornton, J.M.4
  • 6
    • 84868117026 scopus 로고    scopus 로고
    • Prediction of Enzyme Catalytic Sites from Sequence Using Neural Networks; 2007 1-5 April
    • Pande S, Raheja A, Livesay DR, (2007) Prediction of Enzyme Catalytic Sites from Sequence Using Neural Networks; 2007 1-5 April. 2007: 247-253.
    • (2007) , vol.2007 , pp. 247-253
    • Pande, S.1    Raheja, A.2    Livesay, D.R.3
  • 7
    • 40049091146 scopus 로고    scopus 로고
    • Prediction of protein functional residues from sequence by probability density estimation
    • Fischer JD, Mayer CE, Soding J, (2008) Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 24: 613-620.
    • (2008) Bioinformatics , vol.24 , pp. 613-620
    • Fischer, J.D.1    Mayer, C.E.2    Soding, J.3
  • 8
    • 0036384350 scopus 로고    scopus 로고
    • One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions
    • Nagano N, Orengo C, Thornton J, (2002) One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. Journal of Molecular Biology 321: 741-765.
    • (2002) Journal of Molecular Biology , vol.321 , pp. 741-765
    • Nagano, N.1    Orengo, C.2    Thornton, J.3
  • 9
    • 0029973830 scopus 로고    scopus 로고
    • Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases
    • Wallace AC, Laskowski RA, Thornton JM, (1996) Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein science: a publication of the Protein Society 5: 1001-1013.
    • (1996) Protein Science: A Publication of the Protein Society , vol.5 , pp. 1001-1013
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 11
    • 22444434743 scopus 로고    scopus 로고
    • Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces
    • Ben-Shimon A, Eisenstein M, (2005) Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces. J Mol Biol 351: 309-326.
    • (2005) J Mol Biol , vol.351 , pp. 309-326
    • Ben-Shimon, A.1    Eisenstein, M.2
  • 13
    • 34250671141 scopus 로고    scopus 로고
    • Selective prediction of interaction sites in protein structures with THEMATICS
    • Wei Y, Ko J, Murga L, Ondrechen MJ, (2007) Selective prediction of interaction sites in protein structures with THEMATICS. BMC Bioinformatics 8: 119.
    • (2007) BMC Bioinformatics , vol.8 , pp. 119
    • Wei, Y.1    Ko, J.2    Murga, L.3    Ondrechen, M.J.4
  • 14
    • 59149090849 scopus 로고    scopus 로고
    • Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
    • Tong W, Wei Y, Murga LF, Ondrechen MJ, Williams RJ, (2009) Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties. PLoS Comput Biol 5: e1000266.
    • (2009) PLoS Comput Biol , vol.5
    • Tong, W.1    Wei, Y.2    Murga, L.F.3    Ondrechen, M.J.4    Williams, R.J.5
  • 15
    • 77951192988 scopus 로고    scopus 로고
    • Automatic prediction of catalytic residues by modeling residue structural neighborhood
    • Cilia E, Passerini A, (2010) Automatic prediction of catalytic residues by modeling residue structural neighborhood. BMC Bioinformatics 11: 115.
    • (2010) BMC Bioinformatics , vol.11 , pp. 115
    • Cilia, E.1    Passerini, A.2
  • 16
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    • Porter CT, Bartlett GJ, Thornton JM, (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Research 32: D129-D133.
    • (2004) Nucleic Acids Research , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 19
    • 80052257762 scopus 로고    scopus 로고
    • On the relationship between catalytic residues and their protein contact number
    • Huang SW, Yu SH, Shih CH, Guan HW, Huang TT, et al. (2011) On the relationship between catalytic residues and their protein contact number. Curr Protein Pept Sci 12: 574-579.
    • (2011) Curr Protein Pept Sci , vol.12 , pp. 574-579
    • Huang, S.W.1    Yu, S.H.2    Shih, C.H.3    Guan, H.W.4    Huang, T.T.5
  • 21
    • 33746950964 scopus 로고    scopus 로고
    • Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties
    • Petrova N, Wu C, (2006) Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. BMC Bioinformatics 7: 312.
    • (2006) BMC Bioinformatics , vol.7 , pp. 312
    • Petrova, N.1    Wu, C.2
  • 24
    • 34249308113 scopus 로고    scopus 로고
    • How accurate and statistically robust are catalytic site predictions based on closeness centrality?
    • Chea E, Livesay D, (2007) How accurate and statistically robust are catalytic site predictions based on closeness centrality? BMC Bioinformatics 8: 153.
    • (2007) BMC Bioinformatics , vol.8 , pp. 153
    • Chea, E.1    Livesay, D.2
  • 25
    • 53749083563 scopus 로고    scopus 로고
    • Accurate sequence-based prediction of catalytic residues
    • Zhang T, Zhang H, Chen K, Shen S, Ruan J, et al. (2008) Accurate sequence-based prediction of catalytic residues. Bioinformatics 24: 2329-2338.
    • (2008) Bioinformatics , vol.24 , pp. 2329-2338
    • Zhang, T.1    Zhang, H.2    Chen, K.3    Shen, S.4    Ruan, J.5
  • 26
    • 84865150047 scopus 로고    scopus 로고
    • POOL server: machine learning application for functional site prediction in proteins
    • Somarowthu S, Ondrechen MJ, (2012) POOL server: machine learning application for functional site prediction in proteins. Bioinformatics 28: 2078-2079.
    • (2012) Bioinformatics , vol.28 , pp. 2078-2079
    • Somarowthu, S.1    Ondrechen, M.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.