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Volumn 46, Issue W1, 2018, Pages W438-W442

COACH-D: Improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN; PROTEIN BINDING;

EID: 85050892342     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gky439     Document Type: Article
Times cited : (186)

References (22)
  • 1
    • 84879634846 scopus 로고    scopus 로고
    • Structure determination of membrane proteins by nuclear magnetic resonance spectroscopy
    • Opella, S. J. (2013) Structure determination of membrane proteins by nuclear magnetic resonance spectroscopy. Annu. Rev. Anal. Chem., 6, 305-328.
    • (2013) Annu. Rev. Anal. Chem. , vol.6 , pp. 305-328
    • Opella, S.J.1
  • 2
    • 84952639674 scopus 로고    scopus 로고
    • Crosslinking and mass Spectrometry: An integrated technology to understand the structure and function of molecular machines
    • Leitner, A., Faini, M., Stengel, F. and Aebersold, R. (2016) Crosslinking and mass Spectrometry: An integrated technology to understand the structure and function of molecular machines. Trends Biochem. Sci., 41, 20-32.
    • (2016) Trends Biochem. Sci. , vol.41 , pp. 20-32
    • Leitner, A.1    Faini, M.2    Stengel, F.3    Aebersold, R.4
  • 4
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski, M. and Skolnick, J. (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc. Natl. Acad. Sci. U. S. A., 105, 129-134.
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 5
    • 74549149999 scopus 로고    scopus 로고
    • Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
    • Capra, J. A., Laskowski, R. A., Thornton, J. M., Singh, M. and Funkhouser, T. A. (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 , pp. e1000585
    • Capra, J.A.1    Laskowski, R.A.2    Thornton, J.M.3    Singh, M.4    Funkhouser, T.A.5
  • 6
    • 84864460609 scopus 로고    scopus 로고
    • COFACTOR: An accurate comparative algorithm for structure-based protein function annotation
    • Roy, A., Yang, J. and Zhang, Y. (2012) COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res., 40, W471-W477.
    • (2012) Nucleic Acids Res. , vol.40 , pp. W471-W477
    • Roy, A.1    Yang, J.2    Zhang, Y.3
  • 7
    • 84885655034 scopus 로고    scopus 로고
    • Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment
    • Yang, J., Roy, A. and Zhang, Y. (2013) Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 29, 2588-2595.
    • (2013) Bioinformatics , vol.29 , pp. 2588-2595
    • Yang, J.1    Roy, A.2    Zhang, Y.3
  • 8
    • 84904823376 scopus 로고    scopus 로고
    • GalaxySite: Ligand-binding-site prediction by using molecular docking
    • Heo, L., Shin, W. H., Lee, M. S. and Seok, C. (2014) GalaxySite: ligand-binding-site prediction by using molecular docking. Nucleic Acids Res., 42, W210-W214.
    • (2014) Nucleic Acids Res. , vol.42 , pp. W210-W214
    • Heo, L.1    Shin, W.H.2    Lee, M.S.3    Seok, C.4
  • 9
    • 84883574367 scopus 로고    scopus 로고
    • The FunFOLD2 server for the prediction of protein-ligand interactions
    • Roche, D. B., Buenavista, M. T. and McGuffin, L. J. (2013) The FunFOLD2 server for the prediction of protein-ligand interactions. Nucleic Acids Res., 41, W303-W307.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W303-W307
    • Roche, D.B.1    Buenavista, M.T.2    McGuffin, L.J.3
  • 10
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott, O. and Olson, A. J. (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 31, 455-461.
    • (2010) J. Comput. Chem. , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 11
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
    • Huang, S. Y. and Zou, X. (2007) Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins, 66, 399-421.
    • (2007) Proteins , vol.66 , pp. 399-421
    • Huang, S.Y.1    Zou, X.2
  • 13
    • 84871604119 scopus 로고    scopus 로고
    • GalaxyDock: Protein-ligand docking with flexible protein side-chains
    • Shin, W. H. and Seok, C. (2012) GalaxyDock: protein-ligand docking with flexible protein side-chains. J. Chem. Inf. Model., 52, 3225-3232.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 3225-3232
    • Shin, W.H.1    Seok, C.2
  • 14
    • 85013653033 scopus 로고    scopus 로고
    • Forging the basis for developing protein-ligand interaction scoring functions
    • Liu, Z., Su, M., Han, L., Liu, J., Yang, Q., Li, Y. and Wang, R. (2017) Forging the basis for developing protein-ligand interaction scoring functions. Acc. Chem. Res., 50, 302-309.
    • (2017) Acc. Chem. Res. , vol.50 , pp. 302-309
    • Liu, Z.1    Su, M.2    Han, L.3    Liu, J.4    Yang, Q.5    Li, Y.6    Wang, R.7
  • 15
    • 85018596195 scopus 로고    scopus 로고
    • Structural and sequence similarity makes a significant impact on machine-learning-based scoring functions for protein-ligand interactions
    • Li, Y. and Yang, J. (2017) Structural and sequence similarity makes a significant impact on machine-learning-based scoring functions for protein-ligand interactions. J. Chem. Inf. Model., 57, 1007-1012.
    • (2017) J. Chem. Inf. Model. , vol.57 , pp. 1007-1012
    • Li, Y.1    Yang, J.2
  • 16
    • 84883481556 scopus 로고    scopus 로고
    • The protein model Portal-a comprehensive resource for protein structure and model information
    • Haas, J., Roth, S., Arnold, K., Kiefer, F., Schmidt, T., Bordoli, L. and Schwede, T. (2013) The protein model Portal-a comprehensive resource for protein structure and model information. Database, 2013, bat031.
    • (2013) Database , vol.2013 , pp. bat031
    • Haas, J.1    Roth, S.2    Arnold, K.3    Kiefer, F.4    Schmidt, T.5    Bordoli, L.6    Schwede, T.7
  • 17
    • 84925156346 scopus 로고    scopus 로고
    • The I-TASSER Suite: Protein structure and function prediction
    • Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J. and Zhang, Y. (2015) The I-TASSER Suite: protein structure and function prediction. Nat. Methods, 12, 7-8.
    • (2015) Nat. Methods , vol.12 , pp. 7-8
    • Yang, J.1    Yan, R.2    Roy, A.3    Xu, D.4    Poisson, J.5    Zhang, Y.6
  • 18
    • 84876574278 scopus 로고    scopus 로고
    • BioLiP: A semi-manually curated database for biologically relevant ligand-protein interactions
    • Yang, J., Roy, A. and Zhang, Y. (2013) BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res., 41, D1096-D1103.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D1096-D1103
    • Yang, J.1    Roy, A.2    Zhang, Y.3
  • 20
    • 84927720583 scopus 로고    scopus 로고
    • 3Dmol. Js: Molecular visualization with WebGL
    • Rego, N. and Koes, D. (2015) 3Dmol. js: molecular visualization with WebGL. Bioinformatics, 31, 1322-1324.
    • (2015) Bioinformatics , vol.31 , pp. 1322-1324
    • Rego, N.1    Koes, D.2
  • 21
    • 78149275853 scopus 로고    scopus 로고
    • The binding site distance test score: A robust method for the assessment of predicted protein binding sites
    • Roche, D. B., Tetchner, S. J. and McGuffin, L. J. (2010) The binding site distance test score: a robust method for the assessment of predicted protein binding sites. Bioinformatics, 26, 2920-2921.
    • (2010) Bioinformatics , vol.26 , pp. 2920-2921
    • Roche, D.B.1    Tetchner, S.J.2    McGuffin, L.J.3
  • 22
    • 84864448769 scopus 로고    scopus 로고
    • Template-based protein structure modeling using the RaptorX web server
    • Kallberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H. and Xu, J. (2012) Template-based protein structure modeling using the RaptorX web server. Nat. Protoc., 7, 1511-1522.
    • (2012) Nat. Protoc. , vol.7 , pp. 1511-1522
    • Kallberg, M.1    Wang, H.2    Wang, S.3    Peng, J.4    Wang, Z.5    Lu, H.6    Xu, J.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.