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Volumn 42, Issue 21, 1999, Pages 4422-4433

Two-stage method for protein-ligand docking

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN; THROMBIN;

EID: 0032698681     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm991090p     Document Type: Article
Times cited : (78)

References (39)
  • 2
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell, D.; Olson, A. Automated Docking of Substrates to Proteins by Simulated Annealing. PROTEINS: Struct. Funct. Genet. 1990, 8, 195-202.
    • (1990) PROTEINS: Struct. Funct. Genet. , vol.8 , pp. 195-202
    • Goodsell, D.1    Olson, A.2
  • 3
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
    • Welch, W.; Ruppert, J.; Jain, A. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 1996, 3, 449-462.
    • (1996) Chem. Biol. , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.3
  • 4
    • 0030599010 scopus 로고    scopus 로고
    • Predicting receptor-ligand interactions by an incremental construction algorithm
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. Predicting Receptor-Ligand Interactions by 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.4
  • 5
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, P.; Glen, R.; Leach, A.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking. J. Mol. Biol. 1997, 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.3    Leach, A.4    Taylor, R.5
  • 7
    • 0031181870 scopus 로고    scopus 로고
    • Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention
    • Rarey, M.; Kramer, B.; Lengauer, T. Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention. J. Comput.-Aided Mol. Des. 1997, 11, 369-384.
    • (1997) J. Comput.-aided Mol. Des. , vol.11 , pp. 369-384
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 8
    • 0029019869 scopus 로고
    • A continuum model for protein-protein interactions: Application to the docking problem
    • Jackson, R. M.; Sternberg, M. J. E. A Continuum Model for Protein-Protein Interactions: Application to the Docking Problem. J. Mol. Biol. 1995, 250, 258-275.
    • (1995) J. Mol. Biol. , vol.250 , pp. 258-275
    • Jackson, R.M.1    Sternberg, M.J.E.2
  • 9
    • 0030120054 scopus 로고    scopus 로고
    • Orientational sampling and rigid-body minimization in molecular docking revisited: On-the-fly optimization and degeneracy removal
    • Gschwend, D. A.; Kuntz, I. D. Orientational sampling and rigid-body minimization in molecular docking revisited: On-the-fly optimization and degeneracy removal. J. Comput. Aid. Mol. Design 1996, 10, 123-132.
    • (1996) J. Comput. Aid. Mol. Design , vol.10 , pp. 123-132
    • Gschwend, D.A.1    Kuntz, I.D.2
  • 11
    • 0345102881 scopus 로고    scopus 로고
    • Tackling concrete problems in molecular biophysics using monte carlo and related methods: Glycosylation, folding, solvation
    • Grassberger, P., Barkema, G., Nadler, W., Eds.; World Scientific: Singapore, ISBN 981-02-3658-1
    • Hoffmann, D.; Washio, T.; Gessler, K.; Jacob, J. Tackling Concrete Problems in Molecular Biophysics Using Monte Carlo and Related Methods: Glycosylation, Folding, Solvation. In Proceedings of the workshop on: Monte Carlo approach to Biopolymers and Protein Folding; Grassberger, P., Barkema, G., Nadler, W., Eds.; World Scientific: Singapore, 1998; pp 153-170; ISBN 981-02-3658-1.
    • (1998) Proceedings of the Workshop On: Monte Carlo Approach to Biopolymers and Protein Folding , pp. 153-170
    • Hoffmann, D.1    Washio, T.2    Gessler, K.3    Jacob, J.4
  • 12
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Böhm, H.-J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 243-256.
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 243-256
    • Böhm, H.-J.1
  • 13
    • 0030847766 scopus 로고    scopus 로고
    • Protein data bank archives of three-dimensional macromolecular structures
    • Sweet, R. M., Ed.; Academic Press: San Diego
    • Abola, E. E.; Sussman, J. L.; Prilusky, J.; Manning, N. O. Protein Data Bank Archives of Three-Dimensional Macromolecular Structures. In Methods in Enzymology; Sweet, R. M., Ed.; Academic Press: San Diego, 1997; pp 556-571.
    • (1997) Methods in Enzymology , pp. 556-571
    • Abola, E.E.1    Sussman, J.L.2    Prilusky, J.3    Manning, N.O.4
  • 14
    • 0032214622 scopus 로고    scopus 로고
    • Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules
    • Sussman, J. L.; Lin, D.; Jiang, J.; Manning, N. O.; Prilusky, J.; Ritter, O.; Abola, E. E. Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules. Acta Crystallogr. 1998, D54, 1078-1084.
    • (1998) Acta Crystallogr. , vol.D54 , pp. 1078-1084
    • Sussman, J.L.1    Lin, D.2    Jiang, J.3    Manning, N.O.4    Prilusky, J.5    Ritter, O.6    Abola, E.E.7
  • 15
    • 0020475509 scopus 로고
    • Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
    • Warwicker, J.; Watson, H. C. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J. Mol. Biol. 1982, 157, 671-679.
    • (1982) J. Mol. Biol. , vol.157 , pp. 671-679
    • Warwicker, J.1    Watson, H.C.2
  • 16
    • 0022964504 scopus 로고
    • Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification
    • Klapper, I.; Hagstrom, R.; Fine, R.; Honig, B. Focusing of Electric Fields in the Active Site of Cu-Zn Superoxide Dismutase: Effects of Ionic Strength and Amino-Acid Modification. Proteins: Struct. Funct. Genet. 1986, 1, 47-59.
    • (1986) Proteins: Struct. Funct. Genet. , vol.1 , pp. 47-59
    • Klapper, I.1    Hagstrom, R.2    Fine, R.3    Honig, B.4
  • 17
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig, B.; Nicholls, A. Classical Electrostatics in Biology and Chemistry. Science 1995, 268, 1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 18
    • 0011930746 scopus 로고
    • Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area
    • Hermann, R. B. Theory of Hydrophobic Bonding. II. The Correlation of Hydrocarbon Solubility in Water with Solvent Cavity Surface Area. J. Phys. Chem. 1972, 76, 2754.
    • (1972) J. Phys. Chem. , vol.76 , pp. 2754
    • Hermann, R.B.1
  • 19
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg, D.; McLachlan, A. D. Solvation energy in protein folding and binding. Nature 1986, 319, 199-203.
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 20
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • Ooi, T.; Oobatake, M.; Nemethy, G.; Scheraga, H. A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 3086-3090.
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Nemethy, G.3    Scheraga, H.A.4
  • 21
    • 0025668794 scopus 로고
    • Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue
    • Scott, D. L.; Otwinowski, Z.; Gelb, M. H.; Sigler, P. B. Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue. Science 1990, 250, 1563-1566.
    • (1990) Science , vol.250 , pp. 1563-1566
    • Scott, D.L.1    Otwinowski, Z.2    Gelb, M.H.3    Sigler, P.B.4
  • 22
    • 0027377778 scopus 로고
    • Escherichia coli-derived rat intestinal fatty acid binding protein with bound myristate at 1.5 Å resolution and I-FABP with bound oleate at 1.74 Å resolution
    • Eads, J.; Sacchettini, J. C.; Kromminga, A.; Gordon, J. I. Escherichia coli-derived Rat Intestinal Fatty Acid Binding Protein with Bound Myristate at 1.5 Å Resolution and I-FABP with Bound Oleate at 1.74 Å Resolution. J. Biol. Chem. 1993, 268, 26375-26385.
    • (1993) J. Biol. Chem. , vol.268 , pp. 26375-26385
    • Eads, J.1    Sacchettini, J.C.2    Kromminga, A.3    Gordon, J.I.4
  • 23
    • 0025197061 scopus 로고
    • α's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • α's of Ionizable Groups in Proteins: Atomic Detail from a Continuum Electrostatic Model. Biochemistry 1990, 29, 10219-10225.
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 25
    • 0025304137 scopus 로고
    • Refinement of the influenza virus hemagglutinin by simulated annealing
    • Weis, W. I.; Brünger, A. T.; Skehel, J. J.; Wiley: D. C. Refinement of the influenza virus hemagglutinin by simulated annealing. J. Mol. Biol. 1990, 212, 737-761.
    • (1990) J. Mol. Biol. , vol.212 , pp. 737-761
    • Weis, W.I.1    Brünger, A.T.2    Skehel, J.J.3    Wiley, D.C.4
  • 26
    • 0025837452 scopus 로고
    • Crystallographic analysis at 3.0-Å resolution of the binding to human thrombin of four active site-directed inhibitors
    • Banner, D. W.; Hadvary, P. Crystallographic analysis at 3.0-Å resolution of the binding to human thrombin of four active site-directed inhibitors. J. Biol. Chem. 1991, 266, 20085-20093.
    • (1991) J. Biol. Chem. , vol.266 , pp. 20085-20093
    • Banner, D.W.1    Hadvary, P.2
  • 27
    • 0020527888 scopus 로고
    • Cyclic amides of N alpha-arylsulfonylaminoacylated 4-amidinophenylalanine-tight binding inhibitors of thrombin
    • Stürzebecher, J.; Markwardt, F.; Voigt, B.; Wagner, G.; Walsmann, P. Cyclic amides of N alpha-arylsulfonylaminoacylated 4-amidinophenylalanine-tight binding inhibitors of thrombin. Thromb. Res. 1983, 29, 635-642.
    • (1983) Thromb. Res. , vol.29 , pp. 635-642
    • Stürzebecher, J.1    Markwardt, F.2    Voigt, B.3    Wagner, G.4    Walsmann, P.5
  • 28
    • 0028330521 scopus 로고
    • Local and transmitted conformational changes on complexation of an anti-sweetener Fab
    • Guddat, L. W.; Shan, L.; Anchin, J. M.; Linthicum, D. S.; Edmundson, A. B. Local and transmitted conformational changes on complexation of an anti-sweetener Fab. J. Mol. Biol. 1994, 236, 247-274.
    • (1994) J. Mol. Biol. , vol.236 , pp. 247-274
    • Guddat, L.W.1    Shan, L.2    Anchin, J.M.3    Linthicum, D.S.4    Edmundson, A.B.5
  • 29
    • 0022032207 scopus 로고
    • On the specificity of antibody/antigen interactions: Phosphocholine binding to McPC603 and the correlation of three-dimensional structure and sequence data
    • Padlan, E. A.; Cohen, G. H.; Davies, D. R. On the specificity of antibody/antigen interactions: phosphocholine binding to McPC603 and the correlation of three-dimensional structure and sequence data. Ann. Inst. Pasteur. Immunol. 1985, 136C, 271-276.
    • (1985) Ann. Inst. Pasteur. Immunol. , vol.136 C , pp. 271-276
    • Padlan, E.A.1    Cohen, G.H.2    Davies, D.R.3
  • 31
    • 0028519286 scopus 로고
    • Prediction of new serine proteinase inhibitors
    • Kurinov, I. V.; Harrison, R. W. Prediction of new serine proteinase inhibitors. Nat. Struct. Biol. 1994, 1, 735-743.
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 735-743
    • Kurinov, I.V.1    Harrison, R.W.2
  • 32
    • 0026475945 scopus 로고
    • Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography
    • Bocskei, Z.; Flower, D. R.; Groom, C. R.; Phillips, S. E. V.; North, A. C. T. Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography. Nature 1992, 360, 186-188.
    • (1992) Nature , vol.360 , pp. 186-188
    • Bocskei, Z.1    Flower, D.R.2    Groom, C.R.3    Phillips, S.E.V.4    North, A.C.T.5
  • 36
    • 0029092861 scopus 로고
    • Crystal structure of a peptidyl pyridinium methyl ketone inhibitor with thrombin
    • Rehse, P. H.; Steinmetzer, T.; Li, Y.; Konishi, Y.; Cygler, M. Crystal structure of a peptidyl pyridinium methyl ketone inhibitor with thrombin. Biochemistry 1995, 34, 11537-11544.
    • (1995) Biochemistry , vol.34 , pp. 11537-11544
    • Rehse, P.H.1    Steinmetzer, T.2    Li, Y.3    Konishi, Y.4    Cygler, M.5
  • 37
    • 0032961895 scopus 로고
    • The particle concept: Placing discrete water molecules during protein-ligand docking predictions
    • Rarey, M.; Kramer, B.; Lengauer, T. The Particle Concept: Placing discrete water molecules during protein-ligand docking predictions. Proteins: Struct. Funct. Genet. 1990, 34, 17-28.
    • (1990) Proteins: Struct. Funct. Genet. , vol.34 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 38
    • 0031804609 scopus 로고    scopus 로고
    • Inhibitors of HIV-1 protease: A major success of structure-assisted drug design
    • Wlodawer, A.; Vondrasek, J. Inhibitors of HIV-1 Protease: A major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 249-284.
    • (1998) Annu. Rev. Biophys. Biomol. Struct. , vol.27 , pp. 249-284
    • Wlodawer, A.1    Vondrasek, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.