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Volumn 62, Issue 4, 2006, Pages 934-946

PSI-DOCK: Towards highly efficient and accurate flexible ligand docking

Author keywords

Docking, SCORE 3.0; Drug design; Message passing interface (MPI); PSI DOCK; Scoring; Virtual screening

Indexed keywords

DOCKING PROTEIN;

EID: 33644843080     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20790     Document Type: Article
Times cited : (50)

References (30)
  • 1
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing TJA, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput-Aided Mol Des 2001;15:411-428.
    • (2001) J Comput-Aided Mol des , vol.15 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 3
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M, Kramer B, Lengauer T, Klebe GA. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470-489.
    • (1996) J Mol Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.A.4
  • 4
    • 0032533791 scopus 로고    scopus 로고
    • Flexible docking using tabu search and an empirical estimate of binding affinity
    • Baxter CA, Murray CW, Clark DE, Westhead DR, Eldridge MD. Flexible docking using tabu search and an empirical estimate of binding affinity. Proteins 1998;33:367-382.
    • (1998) Proteins , vol.33 , pp. 367-382
    • Baxter, C.A.1    Murray, C.W.2    Clark, D.E.3    Westhead, D.R.4    Eldridge, M.D.5
  • 6
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a generic algorithm and an empirical binding free energy function
    • Jones G, Wilett P, Glen RC, Leach AR, Taylor R. Development and validation of a generic algorithm and an empirical binding free energy function. J Mol Biol 1997;267:727-748.
    • (1997) J Mol Biol , vol.267 , pp. 727-748
    • Jones, G.1    Wilett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 7
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: A novle method for the shape-directed rapid docking of ligands to protein active sites
    • Venkatachalam CM, Jiang X, Oldfield T, Waldman M. LigandFit: a novle method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 2003;21:289-307.
    • (2003) J Mol Graph Model , vol.21 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 8
    • 0031302358 scopus 로고    scopus 로고
    • Flexible protein-ligand docking by global energy optimization in internal coordinates
    • Totrov M, Abagyan R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 1997;Suppl 1:215-220.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 215-220
    • Totrov, M.1    Abagyan, R.2
  • 9
    • 1642350394 scopus 로고    scopus 로고
    • Recent development and application of virtual screening in drug discovery: An overview
    • Hou TJ, Xu XJ. Recent development and application of virtual screening in drug discovery: an overview. Curr Pharm Des 2004;10: 1011-1033.
    • (2004) Curr Pharm des , vol.10 , pp. 1011-1033
    • Hou, T.J.1    Xu, X.J.2
  • 10
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FlexX increamental construction algorithm for protein-ligand docking
    • Kramer B, Rarey M, Lengauer T. Evaluation of the FlexX increamental construction algorithm for protein-ligand docking. Proteins 1999;37:228-241.
    • (1999) Proteins , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 12
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • Kontoyianni M, McClellan LM, Sokol GS. Evaluation of docking performance: comparative data on docking algorithms. J Med Chem 2004;47:558-565.
    • (2004) J Med Chem , vol.47 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 13
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola E, Waters WP, Charifson PS. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 2004;56:235-249.
    • (2004) Proteins , vol.56 , pp. 235-249
    • Perola, E.1    Waters, W.P.2    Charifson, P.S.3
  • 16
    • 0032885355 scopus 로고    scopus 로고
    • Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search
    • Hou TJ, Wang JM, Chen LR, Xu XJ. Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search. Protein Eng 1999;12:639-647.
    • (1999) Protein Eng , vol.12 , pp. 639-647
    • Hou, T.J.1    Wang, J.M.2    Chen, L.R.3    Xu, X.J.4
  • 17
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
    • Wang RX, Liu L, Lai LH, Tang YQ. SCORE: a new empirical method for estimating the binding affinity of a protein-ligand complex. J Mol Model 1998;4:379-394.
    • (1998) J Mol Model , vol.4 , pp. 379-394
    • Wang, R.X.1    Liu, L.2    Lai, L.H.3    Tang, Y.Q.4
  • 18
    • 0842332235 scopus 로고    scopus 로고
    • A practical approach to docking of zinc metalloproteinase inhibitors
    • Hu X, Balaz S, Shelver WH. A practical approach to docking of zinc metalloproteinase inhibitors. J Mol Graph Mod 2004;22:293-307.
    • (2004) J Mol Graph Mod , vol.22 , pp. 293-307
    • Hu, X.1    Balaz, S.2    Shelver, W.H.3
  • 19
    • 1642378145 scopus 로고    scopus 로고
    • Virtual screening for kinase targets
    • Muegge I, Enyedy IJ. Virtual screening for kinase targets. Curr Med Chem 2004;11:693-707.
    • (2004) Curr Med Chem , vol.11 , pp. 693-707
    • Muegge, I.1    Enyedy, I.J.2
  • 20
    • 0041376417 scopus 로고    scopus 로고
    • Docking and biological activity of pteridine analogs: Search for inhibitors of pteridine reductase enzymes from Trypanosoma cruzi
    • Schormann N, Senkovich O, Ananthan S, Chattopadhyay D. Docking and biological activity of pteridine analogs: search for inhibitors of pteridine reductase enzymes from Trypanosoma cruzi. J Mol Struct-Theochem 2003;635:37-44.
    • (2003) J Mol Struct-Theochem , vol.635 , pp. 37-44
    • Schormann, N.1    Senkovich, O.2    Ananthan, S.3    Chattopadhyay, D.4
  • 21
  • 22
    • 10344264422 scopus 로고    scopus 로고
    • Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation
    • Pei JF, Wang Q, Zhou JJ, Lai LH. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation. Proteins 2004;57: 651-664.
    • (2004) Proteins , vol.57 , pp. 651-664
    • Pei, J.F.1    Wang, Q.2    Zhou, J.J.3    Lai, L.H.4
  • 23
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang RX, Lai LH, Wang SM. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput-Aided Mol Des 2002;16:11-26.
    • (2002) J Comput-Aided Mol des , vol.16 , pp. 11-26
    • Wang, R.X.1    Lai, L.H.2    Wang, S.M.3
  • 24
    • 0141474826 scopus 로고    scopus 로고
    • St, Louis MO: Tripos Associates
    • SYBYL, version 6.9. St, Louis MO: Tripos Associates; 2004.
    • (2004) SYBYL, Version 6.9
  • 25
    • 84986483798 scopus 로고
    • The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
    • Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M. The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J Comput Chem 1995;16:273-284.
    • (1995) J Comput Chem , vol.16 , pp. 273-284
    • Eisenhaber, F.1    Lijnzaad, P.2    Argos, P.3    Sander, C.4    Scharf, M.5
  • 26
    • 84913591509 scopus 로고
    • Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency
    • Eisenhaber F, Argos P, Improved strategy in analytic surface calculation for molecular systems: handling of singularities and computational efficiency. J Comput Chem 1993;14:1272-1280.
    • (1993) J Comput Chem , vol.14 , pp. 1272-1280
    • Eisenhaber, F.1    Argos, P.2
  • 28
    • 2942519283 scopus 로고    scopus 로고
    • Assessment of multiple binding modes in ligand-protein docking
    • Källblad P, Mancera RL, Todorov NP. Assessment of multiple binding modes in ligand-protein docking. J Med Chem 2004;47: 3334-3337.
    • (2004) J Med Chem , vol.47 , pp. 3334-3337
    • Källblad, P.1    Mancera, R.L.2    Todorov, N.P.3
  • 29
    • 0141506108 scopus 로고    scopus 로고
    • Protein Ligand Database (PLD): Additional understanding of the nature and specificity of protein-ligand complexes
    • Puvanendrampillai D, Mitchell JBO. Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics 2003;19:1856-1857.
    • (2003) Bioinformatics , vol.19 , pp. 1856-1857
    • Puvanendrampillai, D.1    Mitchell, J.B.O.2
  • 30
    • 0036467249 scopus 로고    scopus 로고
    • Potential of mean force field for protein-protein interaction studies
    • Jiang L, Gao Y, Mao FL, Liu ZJ, Lai LH. Potential of mean force field for protein-protein interaction studies. Proteins 2002;46:190-196.
    • (2002) Proteins , vol.46 , pp. 190-196
    • Jiang, L.1    Gao, Y.2    Mao, F.L.3    Liu, Z.J.4    Lai, L.H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.