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Volumn 27, Issue 15, 2011, Pages 2083-2088

Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 79960395595     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr331     Document Type: Article
Times cited : (275)

References (27)
  • 1
    • 0041989751 scopus 로고    scopus 로고
    • CASTp: Computed Atlas of Surface Topography of proteins
    • Binkowski,T.A. et al. (2003) CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Res., 31, 3352-3355.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3352-3355
    • Binkowski, T.A.1
  • 2
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • Brady,G.P. Jr and Stouten,P.F. (2000) Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des., 14, 383-401.
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.2
  • 3
    • 74549149999 scopus 로고    scopus 로고
    • Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
    • Capra,J.A. et al. (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput. Biol., 5, e1000585.
    • (2009) PLoS Comput. Biol. , vol.5
    • Capra, J.A.1
  • 4
    • 33846155913 scopus 로고    scopus 로고
    • Structure-based maximal affinity model predicts smallmolecule druggability
    • Cheng,A.C. et al. (2007) Structure-based maximal affinity model predicts smallmolecule druggability. Nat. Biotechnol., 25, 71-75.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 71-75
    • Cheng, A.C.1
  • 5
    • 33747818007 scopus 로고    scopus 로고
    • CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    • Dundas,J. et al. (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res., 34, W116-W118.
    • (2006) Nucleic Acids Res. , vol.34
    • Dundas, J.1
  • 7
    • 75949102748 scopus 로고    scopus 로고
    • EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures
    • Ghersi,D. and Sanchez,R. (2009) EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures. Bioinformatics, 25, 3185-3186.
    • (2009) Bioinformatics , vol.25 , pp. 3185-3186
    • Ghersi, D.1    Sanchez, R.2
  • 8
    • 17144373303 scopus 로고    scopus 로고
    • Druggability indices for protein targets derived from NMRbased screening data
    • Hajduk,P.J. et al. (2005a) Druggability indices for protein targets derived from NMRbased screening data. J. Med. Chem., 48, 2518-2525.
    • (2005) J. Med. Chem. , vol.48 , pp. 2518-2525
    • Hajduk, P.J.1
  • 9
    • 29144483936 scopus 로고    scopus 로고
    • Predicting protein druggability
    • Hajduk,P.J. et al. (2005b) Predicting protein druggability. Drug Discov. Today, 10, 1675-1682.
    • (2005) Drug Discov. Today , vol.10 , pp. 1675-1682
    • Hajduk, P.J.1
  • 10
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
    • Hendlich,M. et al. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model., 15, 359-363.
    • (1997) J. Mol. Graph. Model. , vol.15 , pp. 359-363
    • Hendlich, M.1
  • 11
    • 67849097355 scopus 로고    scopus 로고
    • SITEHOUND-web: a server for ligand binding site identification in protein structures
    • Hernandez,M. et al. (2009) SITEHOUND-web: a server for ligand binding site identification in protein structures. Nucleic Acids Res., 37, W413-W416.
    • (2009) Nucleic Acids Res. , vol.37
    • Hernandez, M.1
  • 12
    • 69249150494 scopus 로고    scopus 로고
    • MetaPocket: a meta approach to improve protein ligand binding site prediction
    • Huang,B. (2009) MetaPocket: a meta approach to improve protein ligand binding site prediction. OMICS, 13, 325-330.
    • (2009) OMICS , vol.13 , pp. 325-330
    • Huang, B.1
  • 13
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation
    • Huang,B. and Schroeder,M. (2006) LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol., 6, 19.
    • (2006) BMC Struct. Biol. , vol.6 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 14
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: a web server for clustering and comparing biological sequences
    • Huang,Y. et al. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680-682.
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1
  • 15
    • 77951217659 scopus 로고    scopus 로고
    • Detection of multiscale pockets on protein surfaces using mathematical morphology
    • Kawabata,T. (2010) Detection of multiscale pockets on protein surfaces using mathematical morphology. Proteins, 78, 1195-1211.
    • (2010) Proteins , vol.78 , pp. 1195-1211
    • Kawabata, T.1
  • 16
    • 34250831648 scopus 로고    scopus 로고
    • Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites
    • Kawabata,T. and Go,N. (2007) Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites. Proteins, 68, 516-529.
    • (2007) Proteins , vol.68 , pp. 516-529
    • Kawabata, T.1    Go, N.2
  • 17
    • 0028881975 scopus 로고
    • SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • 307-308
    • Laskowski,R.A. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph., 13, 323-330, 307-308.
    • (1995) J. Mol. Graph. , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 18
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    • Laurie,A.T. and Jackson,R.M. (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics, 21, 1908-1916.
    • (2005) Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.1    Jackson, R.M.2
  • 19
    • 67649422714 scopus 로고    scopus 로고
    • Fpocket: an open source platform for ligand pocket detection
    • Le Guilloux,V. et al. (2009) Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics, 10, 168.
    • (2009) BMC Bioinformatics , vol.10 , pp. 168
    • Le Guilloux, V.1
  • 20
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li,W. and Godzik,A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 21
    • 33646757492 scopus 로고    scopus 로고
    • On the nature of cavities on protein surfaces: application to the identification of drug-binding sites
    • Nayal,M. and Honig,B. (2006) On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins, 63, 892-906.
    • (2006) Proteins , vol.63 , pp. 892-906
    • Nayal, M.1    Honig, B.2
  • 22
    • 77955397914 scopus 로고    scopus 로고
    • Understanding and predicting druggability. A highthroughput method for detection of drug binding sites
    • Schmidtke,P. and Barril,X. (2010) Understanding and predicting druggability. A highthroughput method for detection of drug binding sites. J. Med. Chem., 53, 5858-5867.
    • (2010) J. Med. Chem. , vol.53 , pp. 5858-5867
    • Schmidtke, P.1    Barril, X.2
  • 23
    • 70349739403 scopus 로고    scopus 로고
    • Assessing the druggability of protein-protein interactions by a supervised machine-learning method
    • Sugaya,N. and Ikeda,K. (2009) Assessing the druggability of protein-protein interactions by a supervised machine-learning method. BMC Bioinformatics, 10, 263.
    • (2009) BMC Bioinformatics , vol.10 , pp. 263
    • Sugaya, N.1    Ikeda, K.2
  • 24
    • 34547341277 scopus 로고    scopus 로고
    • PocketPicker: analysis of ligand binding-sites with shape descriptors
    • Weisel,M. et al. (2007) PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem. Cent. J., 1, 7.
    • (2007) Chem. Cent. J. , vol.1 , pp. 7
    • Weisel, M.1
  • 25
    • 33644876210 scopus 로고    scopus 로고
    • DrugBank: a comprehensive resource for in silico drug discovery and exploration
    • Wishart,D.S. et al. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res., 34, D668-D672.
    • (2006) Nucleic Acids Res. , vol.34
    • Wishart, D.S.1
  • 26
    • 38549151817 scopus 로고    scopus 로고
    • DrugBank: a knowledgebase for drugs, drug actions and drug targets
    • Wishart,D.S. et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 36, D901-D906.
    • (2008) Nucleic Acids Res. , vol.36
    • Wishart, D.S.1
  • 27
    • 75249088440 scopus 로고    scopus 로고
    • Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
    • Yu,J. et al. (2010) Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics, 26, 46-52.
    • (2010) Bioinformatics , vol.26 , pp. 46-52
    • Yu, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.