메뉴 건너뛰기




Volumn 43, Issue W1, 2015, Pages W443-W447

PLIP: Fully automated protein-ligand interaction profiler

Author keywords

[No Author keywords available]

Indexed keywords

CATION; HALOGEN; LIGAND; PROTEIN; SODIUM CHLORIDE; WATER; ENZYME INHIBITOR;

EID: 84979851890     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv315     Document Type: Article
Times cited : (1466)

References (23)
  • 1
    • 37549024654 scopus 로고    scopus 로고
    • The protein data bank: A historical perspective
    • Berman, H.M. (2008) The Protein Data Bank: a historical perspective. Acta Crystallogr. A, 64, 88-95.
    • (2008) Acta Crystallogr. A , vol.64 , pp. 88-95
    • Berman, H.M.1
  • 2
    • 84904818819 scopus 로고    scopus 로고
    • ProBiS-ligands: A web server for prediction of ligands by examination of protein binding sites
    • Konc, J. and Janežič, D. (2014) ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites. Nucleic Acids Res., 42, W215-W220.
    • (2014) Nucleic Acids Res. , vol.42 , pp. W215-W220
    • Konc, J.1    Janežič, D.2
  • 3
    • 84875479590 scopus 로고    scopus 로고
    • Encoding protein-ligand interaction patterns in fingerprints and graphs
    • Desaphy, J., Raimbaud, E., Ducrot, P. and Rognan, D. (2013) Encoding protein-ligand interaction patterns in fingerprints and graphs. J. Chem. Inf. Model., 53, 623-637.
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 623-637
    • Desaphy, J.1    Raimbaud, E.2    Ducrot, P.3    Rognan, D.4
  • 4
    • 84888606432 scopus 로고    scopus 로고
    • Binding affinity prediction for protein-ligand complexes based on beta contacts and B factor
    • Liu, Q., Kwoh, C.K. and Li, J. (2013) Binding affinity prediction for protein-ligand complexes based on beta contacts and B factor. J. Chem. Inf. Model., 53, 3076-3085.
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 3076-3085
    • Liu, Q.1    Kwoh, C.K.2    Li, J.3
  • 5
    • 84924026602 scopus 로고    scopus 로고
    • Polypharmacology rescored: Protein-ligand interaction profiles for remote binding site similarity assessment
    • Salentin, S., Haupt, V.J., Daminelli, S. and Schroeder, M. (2014) Polypharmacology rescored: protein-ligand interaction profiles for remote binding site similarity assessment. Prog. Biophys. Mol. Biol., 116, 174-186.
    • (2014) Prog. Biophys. Mol. Biol. , vol.116 , pp. 174-186
    • Salentin, S.1    Haupt, V.J.2    Daminelli, S.3    Schroeder, M.4
  • 6
    • 79960029361 scopus 로고    scopus 로고
    • SwissDock, a protein-small molecule docking web service based on EADock DSS
    • Grosdidier, A., Zoete, V. and Michielin, O. (2011) SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res., 39, W270-W277.
    • (2011) Nucleic Acids Res. , vol.39 , pp. W270-W277
    • Grosdidier, A.1    Zoete, V.2    Michielin, O.3
  • 7
    • 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
  • 8
    • 84857557833 scopus 로고    scopus 로고
    • ProBiS-database: Precalculated binding site similarities and local pairwise alignments of PDB structures
    • Konc, J., Cesnik, T., Konc, J.T., Penca, M. and Janežič, D. (2012) ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. J. Chem. Inf. Model., 52, 604-612.
    • (2012) J. Chem. Inf. Model , vol.52 , pp. 604-612
    • Konc, J.1    Cesnik, T.2    Konc, J.T.3    Penca, M.4    Janežič, D.5
  • 9
    • 84879269767 scopus 로고    scopus 로고
    • Drug promiscuity in PDB: Protein binding site similarity is key
    • Haupt, V.J., Daminelli, S. and Schroeder, M. (2013) Drug promiscuity in PDB: protein binding site similarity is key. PLoS One, 8, e65894.
    • (2013) PLoS One , vol.8 , pp. e65894
    • Haupt, V.J.1    Daminelli, S.2    Schroeder, M.3
  • 10
    • 79960809682 scopus 로고    scopus 로고
    • Old friends in new guise: Repositioning of known drugs with structural bioinformatics
    • Haupt, V.J. and Schroeder, M. (2011) Old friends in new guise: repositioning of known drugs with structural bioinformatics. Brief Bioinform., 12, 312-326.
    • (2011) Brief Bioinform. , vol.12 , pp. 312-326
    • Haupt, V.J.1    Schroeder, M.2
  • 11
    • 79953277006 scopus 로고    scopus 로고
    • BINANA: A novel algorithm for ligand-binding characterization
    • Durrant, J. and McCammon, J. (2011) BINANA: a novel algorithm for ligand-binding characterization. J. Mol. Graph. Mod., 29, 888-893.
    • (2011) J. Mol. Graph. Mod. , vol.29 , pp. 888-893
    • Durrant, J.1    McCammon, J.2
  • 12
    • 84892389578 scopus 로고    scopus 로고
    • GIANT: Pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes
    • Kasahara, K. and Kinoshita, K. (2014) GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes. BMC Bioinformatics, 15, 12.
    • (2014) BMC Bioinformatics , vol.15 , pp. 12
    • Kasahara, K.1    Kinoshita, K.2
  • 14
    • 58149092163 scopus 로고    scopus 로고
    • CREDO: A protein-ligand interaction database for drug discovery
    • Schreyer, A. and Blundell, T. (2009) CREDO: a protein-ligand interaction database for drug discovery. Chem. Biol. Drug Des., 73, 157-167.
    • (2009) Chem. Biol. Drug Des. , vol.73 , pp. 157-167
    • Schreyer, A.1    Blundell, T.2
  • 15
    • 84873304969 scopus 로고    scopus 로고
    • PLI: A web-based tool for the comparison of protein-ligand interactions observed on PDB structures
    • Gallina, A.M., Bisignano, P., Bergamino, M. and Bordo, D. (2013) PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures. Bioinformatics, 29, 395-397.
    • (2013) Bioinformatics , vol.29 , pp. 395-397
    • Gallina, A.M.1    Bisignano, P.2    Bergamino, M.3    Bordo, D.4
  • 16
    • 0037436339 scopus 로고    scopus 로고
    • Relibase: Design and development of a database for comprehensive analysis of protein-ligand interactions
    • Hendlich, M., Bergner, A., Günther, J. and Klebe, G. (2003) Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J. Mol. Biol., 326, 607-620.
    • (2003) J. Mol. Biol. , vol.326 , pp. 607-620
    • Hendlich, M.1    Bergner, A.2    Günther, J.3    Klebe, G.4
  • 18
    • 80054911951 scopus 로고    scopus 로고
    • LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery
    • Laskowski, R.A. and Swindells, M.B. (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model., 51, 2778-2786.
    • (2011) J. Chem. Inf. Model , vol.51 , pp. 2778-2786
    • Laskowski, R.A.1    Swindells, M.B.2
  • 19
    • 84862847617 scopus 로고    scopus 로고
    • PROLIX: Rapid mining of protein-ligand interactions in large crystal structure databases
    • Weisel, M., Bitter, H.-M., Diederich, F., So, W.V. and Kondru, R. (2012) PROLIX: rapid mining of protein-ligand interactions in large crystal structure databases. J. Chem. Inf. Mod., 52, 1450-1461.
    • (2012) J. Chem. Inf. Mod. , vol.52 , pp. 1450-1461
    • Weisel, M.1    Bitter, H.-M.2    Diederich, F.3    So, W.V.4    Kondru, R.5
  • 20
    • 35248846115 scopus 로고    scopus 로고
    • 2D depiction of protein-ligand complexes
    • Clark, A.M. and Labute, P. (2007) 2D depiction of protein-ligand complexes. J. Chem. Inf. Mod., 47, 1933-1944.
    • (2007) J. Chem. Inf. Mod. , vol.47 , pp. 1933-1944
    • Clark, A.M.1    Labute, P.2
  • 21
    • 41249091782 scopus 로고    scopus 로고
    • Pybel: A python wrapper for the OpenBabel cheminformatics toolkit
    • O'Boyle, N.M., Morley, C. and Hutchison, G.R. (2008) Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. Chem. Cent. J., 2, 5.
    • (2008) Chem. Cent. J. , vol.2 , pp. 5
    • O'Boyle, N.M.1    Morley, C.2    Hutchison, G.R.3
  • 22
    • 84875480305 scopus 로고    scopus 로고
    • Latest developments in molecular docking: 2010-2011 in review
    • Yuriev, E. and Ramsland, P.A. (2013) Latest developments in molecular docking: 2010-2011 in review. J. Mol. Recognit., 26, 215-239.
    • (2013) J. Mol. Recognit. , vol.26 , pp. 215-239
    • Yuriev, E.1    Ramsland, P.A.2
  • 23
    • 79960742823 scopus 로고    scopus 로고
    • Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase
    • Koch, C., Heine, A. and Klebe, G. (2011) Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase. Biochim. Biophys. Acta, 1810, 879-887.
    • (2011) Biochim. Biophys. Acta , vol.1810 , pp. 879-887
    • Koch, C.1    Heine, A.2    Klebe, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.