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Volumn 48, Issue 13, 2005, Pages 4432-4443

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE 2; DOCKING PROTEIN; HEAT SHOCK PROTEIN 90; RECEPTOR PROTEIN;

EID: 21244479779     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm048972v     Document Type: Article
Times cited : (188)

References (65)
  • 2
  • 3
    • 2342586724 scopus 로고    scopus 로고
    • Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding
    • Perola, E.; Charifson, P. S. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J. Med. Chem. 2004, 47, 2499-2510.
    • (2004) J. Med. Chem. , vol.47 , pp. 2499-2510
    • Perola, E.1    Charifson, P.S.2
  • 4
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • Teague, S. J. Implications of protein flexibility for drug discovery. Nat. Rev. Drug Discovery 2003, 2, 527-541.
    • (2003) Nat. Rev. Drug Discovery , vol.2 , pp. 527-541
    • Teague, S.J.1
  • 5
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
    • Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem. 2004, 47, 45-55.
    • (2004) J. Med. Chem. , vol.47 , pp. 45-55
    • Erickson, J.A.1    Jalaie, M.2    Robertson, D.H.3    Lewis, R.A.4    Vieth, M.5
  • 6
    • 0038544571 scopus 로고    scopus 로고
    • Analysis and optimization of structure-based virtual screening protocols (1): Exploration of ligand conformational sampling techniques
    • Good, A. C.; Cheney, D. L. Analysis and optimization of structure-based virtual screening protocols (1): exploration of ligand conformational sampling techniques. J. Mol. Graph. Modell. 2003, 22, 23-30.
    • (2003) J. Mol. Graph. Modell. , vol.22 , pp. 23-30
    • Good, A.C.1    Cheney, D.L.2
  • 7
    • 0742269481 scopus 로고    scopus 로고
    • Automated docking of highly flexible ligands by genetic algorithms: A critical assessment
    • Cecchini, M.; Kolb, P.; Majeux, N.; Caflisch, A. Automated docking of highly flexible ligands by genetic algorithms: a critical assessment. J. Comput. Chem. 2004, 25, 412-422.
    • (2004) J. Comput. Chem. , vol.25 , pp. 412-422
    • Cecchini, M.1    Kolb, P.2    Majeux, N.3    Caflisch, A.4
  • 8
    • 0033974667 scopus 로고    scopus 로고
    • Accommodating protein flexibility in computational drug design
    • Carlson, H. A.; McCammon, J. A. Accommodating protein flexibility in computational drug design. Mol. Pharmacol. 2000, 57, 213-218.
    • (2000) Mol. Pharmacol. , vol.57 , pp. 213-218
    • Carlson, H.A.1    McCammon, J.A.2
  • 9
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach, A. R. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 1994, 235, 345-356.
    • (1994) J. Mol. Biol. , vol.235 , pp. 345-356
    • Leach, A.R.1
  • 10
    • 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, 215-220.
    • (1997) Proteins , pp. 215-220
    • Totrov, M.1    Abagyan, R.2
  • 11
    • 0042282803 scopus 로고    scopus 로고
    • FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function
    • Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. J. Comput. Chem. 2003, 24, 1637-1656.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1637-1656
    • Taylor, R.D.1    Jewsbury, P.J.2    Essex, J.W.3
  • 12
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. Molecular docking to ensembles of protein structures. J. Mol. Biol. 1997, 266, 424-440.
    • (1997) J. Mol. Biol. , vol.266 , pp. 424-440
    • Knegtel, R.M.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 13
    • 0035957528 scopus 로고    scopus 로고
    • FlexE: Efficient molecular docking considering protein structure variations
    • Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. FlexE: efficient molecular docking considering protein structure variations. J. Mol. Biol. 2001, 308, 377-395.
    • (2001) J. Mol. Biol. , vol.308 , pp. 377-395
    • Claussen, H.1    Buning, C.2    Rarey, M.3    Lengauer, T.4
  • 14
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
    • Osterberg, F.; Morris, G. M.; Sanner, M. F.; Olson, A. J.; Goodsell, D. S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002, 46, 34-40.
    • (2002) Proteins , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 15
    • 0037231646 scopus 로고    scopus 로고
    • The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
    • Lin, J. H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003, 68, 47-62.
    • (2003) Biopolymers , vol.68 , pp. 47-62
    • Lin, J.H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4
  • 16
    • 0036462475 scopus 로고    scopus 로고
    • High-throughput crystallization and structure determination in drug discovery
    • Stewart, L.; Clark, R.; Behnke, C. High-throughput crystallization and structure determination in drug discovery. Drug Discovery Today 2002, 7, 187-196.
    • (2002) Drug Discovery Today , vol.7 , pp. 187-196
    • Stewart, L.1    Clark, R.2    Behnke, C.3
  • 18
    • 0032718788 scopus 로고    scopus 로고
    • The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
    • Murray, C. W.; Baxter, C. A.; Frenkel, A. D. The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J. Comput.-Aided Mol. Des 1999, 13, 547-562.
    • (1999) J. Comput.-Aided Mol. Des. , vol.13 , pp. 547-562
    • Murray, C.W.1    Baxter, C.A.2    Frenkel, A.D.3
  • 19
    • 0038460858 scopus 로고    scopus 로고
    • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
    • McGovern, S. L.; Shoichet, B. K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem. 2003, 46, 2895-2907.
    • (2003) J. Med. Chem. , vol.46 , pp. 2895-2907
    • McGovern, S.L.1    Shoichet, B.K.2
  • 20
    • 0037379786 scopus 로고    scopus 로고
    • Ligand-induced conformational changes: Improved predictions of ligand binding conformations and affinities
    • Frimurer, T. M.; Peters, G. H.; Iversen, L. F.; Andersen, H. S.; Moller, N. P.; Olsen, O. H. Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. Biophys. J. 2003, 84, 2273-2281.
    • (2003) Biophys. J. , vol.84 , pp. 2273-2281
    • Frimurer, T.M.1    Peters, G.H.2    Iversen, L.F.3    Andersen, H.S.4    Moller, N.P.5    Olsen, O.H.6
  • 21
    • 1442351132 scopus 로고    scopus 로고
    • Protein flexibility in ligand docking and virtual screening to protein kinases
    • Cavasotto, C. N.; Abagyan, R. A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 2004, 337, 209-225.
    • (2004) J. Mol. Biol. , vol.337 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 22
    • 1842471241 scopus 로고    scopus 로고
    • Testing a flexible-receptor docking algorithm in a model binding site
    • Wei, B. Q.; Weaver, L. H.; Ferrari, A. M.; Matthews, B. W.; Shoichet, B. K. Testing a flexible-receptor docking algorithm in a model binding site. J. Mol. Biol. 2004, 337, 1161-1182.
    • (2004) J. Mol. Biol. , vol.337 , pp. 1161-1182
    • Wei, B.Q.1    Weaver, L.H.2    Ferrari, A.M.3    Matthews, B.W.4    Shoichet, B.K.5
  • 23
    • 4744365803 scopus 로고    scopus 로고
    • Soft docking and multiple receptor conformations in virtual screening
    • in press
    • Ferrari, A. M.; Wei, B. Q.; Constantino, L.; Shoichet, B. K. Soft Docking and Multiple Receptor Conformations in Virtual Screening. J. Med. Chem. 2004, in press.
    • (2004) J. Med. Chem.
    • Ferrari, A.M.1    Wei, B.Q.2    Constantino, L.3    Shoichet, B.K.4
  • 24
    • 0034660892 scopus 로고    scopus 로고
    • The Pezcoller lecture: Cancer cell cycles revisited
    • Sherr, C. J. The Pezcoller lecture: cancer cell cycles revisited. Cancer Res. 2000, 60, 3689-3695.
    • (2000) Cancer Res. , vol.60 , pp. 3689-3695
    • Sherr, C.J.1
  • 26
    • 0035989680 scopus 로고    scopus 로고
    • HSP90 as a new therapeutic target for cancer therapy: The story unfolds
    • Maloney, A.; Workman, P. HSP90 as a new therapeutic target for cancer therapy: the story unfolds. Expert Opin. Biol. Ther. 2002, 2, 3-24.
    • (2002) Expert Opin. Biol. Ther. , vol.2 , pp. 3-24
    • Maloney, A.1    Workman, P.2
  • 27
    • 0141596326 scopus 로고    scopus 로고
    • Clinical development of 17-allylamino, 17-demethoxygeldanamycin
    • Sausville, E. A.; Tomaszewski, J. E.; Ivy, P. Clinical development of 17-allylamino, 17-demethoxygeldanamycin. Curr. Cancer Drug Targets 2003, 3, 377-383.
    • (2003) Curr. Cancer Drug Targets , vol.3 , pp. 377-383
    • Sausville, E.A.1    Tomaszewski, J.E.2    Ivy, P.3
  • 28
    • 0033985080 scopus 로고    scopus 로고
    • GHKL, an emergent ATPase/kinase superfamily
    • Dutta, R.; Inouye, M. GHKL, an emergent ATPase/kinase superfamily. Trends Biochem. Sci. 2000, 25, 24-28.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 24-28
    • Dutta, R.1    Inouye, M.2
  • 29
    • 0030987132 scopus 로고    scopus 로고
    • An atypical topoisomerase II from Archaea with implications for meiotic recombination
    • Bergerat, A.; de Massy, B.; Gadelle, D.; Varoutas, P.C.; Nicolas, A.; Forterre, P. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 1997, 386, 414-417.
    • (1997) Nature , vol.386 , pp. 414-417
    • Bergerat, A.1    De Massy, B.2    Gadelle, D.3    Varoutas, P.C.4    Nicolas, A.5    Forterre, P.6
  • 32
    • 0033668689 scopus 로고    scopus 로고
    • Predicting binding modes, binding affinities and 'hot spots' for protein-ligand complexes using a knowledge-based scoring function
    • Gohlke, H.; Hendlich, M.; Klebe, G. Predicting binding modes, binding affinities and 'hot spots' for protein-ligand complexes using a knowledge-based scoring function. Perspect. Drug Discovery Des. 2000, 20, 115-144.
    • (2000) Perspect. Drug Discovery Des. , vol.20 , pp. 115-144
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 33
    • 2342514226 scopus 로고    scopus 로고
    • Guided docking approaches to structure-based design and screening
    • Fradera, X.; Mestres, J. Guided docking approaches to structure-based design and screening. Curr. Top. Med. Chem. 2004, 4, 687-700.
    • (2004) Curr. Top. Med. Chem. , vol.4 , pp. 687-700
    • Fradera, X.1    Mestres, J.2
  • 34
    • 0034284367 scopus 로고    scopus 로고
    • Similarity-driven flexible ligand docking
    • Fradera, X.; Knegtel, R. M.; Mestres, J. Similarity-driven flexible ligand docking. Proteins 2000, 40, 623-636.
    • (2000) Proteins , vol.40 , pp. 623-636
    • Fradera, X.1    Knegtel, R.M.2    Mestres, J.3
  • 37
  • 38
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • Shoichet, B. K. Virtual screening of chemical libraries. Nature 2004, 432, 862-865.
    • (2004) Nature , vol.432 , pp. 862-865
    • Shoichet, B.K.1
  • 39
    • 0038336897 scopus 로고    scopus 로고
    • Application and limitations of X-ray crystallographic data in structure-based ligand and drug design
    • Davis, A. M.; Teague, S. J.; Kleywegt, G. J. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew. Chem., Int. Ed Engl. 2003, 42, 2718-2736.
    • (2003) Angew. Chem., Int. Ed. Engl. , vol.42 , pp. 2718-2736
    • Davis, A.M.1    Teague, S.J.2    Kleywegt, G.J.3
  • 40
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 1999, 42, 5100-5109.
    • (1999) J. Med. Chem. , vol.42 , pp. 5100-5109
    • Charifson, P.S.1    Corkery, J.J.2    Murcko, M.A.3    Walters, W.P.4
  • 42
    • 21244453582 scopus 로고    scopus 로고
    • Accelrys Inc.: San Diego, CA
    • InsightII, Release 2000; Accelrys Inc.: San Diego, CA, 2002.
    • (2002) InsightII, Release 2000
  • 43
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 1999, 285, 1735-1747.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 44
    • 0029937870 scopus 로고    scopus 로고
    • Hydrophilicity of cavities in proteins
    • Zhang, L.; Hermans, J. Hydrophilicity of cavities in proteins. Proteins 1996, 24, 433-438.
    • (1996) Proteins , vol.24 , pp. 433-438
    • Zhang, L.1    Hermans, J.2
  • 45
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital-electronegativity - A rapid access to atomic charges
    • Gasteiger, J.; Marsili, M. Iterative partial equalization of orbital-electronegativity - A rapid access to atomic charges. Tetrahedron 1980, 36, 3219-3228.
    • (1980) Tetrahedron , vol.36 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 48
    • 0141792684 scopus 로고    scopus 로고
    • Informative library design as an efficient strategy to identify and optimize leads: Application to cyclin-dependent kinase 2 antagonists
    • Bradley, E. K.; Miller, J. L.; Saiah, E.; Grootenhuis, P. D. Informative library design as an efficient strategy to identify and optimize leads: application to cyclin-dependent kinase 2 antagonists. J. Med. Chem. 2003, 46, 4360-4364.
    • (2003) J. Med. Chem. , vol.46 , pp. 4360-4364
    • Bradley, E.K.1    Miller, J.L.2    Saiah, E.3    Grootenhuis, P.D.4
  • 49
    • 31444452744 scopus 로고
    • Automatic generation of 3D-atomic coordinates for organic molecules
    • Gasteiger, J.; Rudolph, C.; Sadowski, J. Automatic Generation of 3D-Atomic Coordinates for Organic Molecules. Tetrahedron Comput. Methodol. 1990, 3, 537-547.
    • (1990) Tetrahedron Comput. Methodol. , vol.3 , pp. 537-547
    • Gasteiger, J.1    Rudolph, C.2    Sadowski, J.3
  • 50
    • 0031005361 scopus 로고    scopus 로고
    • Crystal structure of an Hsp90-geldanamycin complex: Targeting of a protein chaperone by an antitumor agent
    • Stebbins, C. E.; Russo, A. A.; Schneider, C.; Rosen, N.; Hartl, F. U.; Pavletich, N. P. Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent. Cell 1997, 89, 239-250.
    • (1997) Cell , vol.89 , pp. 239-250
    • Stebbins, C.E.1    Russo, A.A.2    Schneider, C.3    Rosen, N.4    Hartl, F.U.5    Pavletich, N.P.6
  • 54
    • 0036939824 scopus 로고    scopus 로고
    • Towards a fully integrated strategy for structure-based drug discovery
    • Knowles, D. Towards a fully integrated strategy for structure-based drug discovery. Curr. Drug Discovery 2002, 31-35.
    • (2002) Curr. Drug Discovery , pp. 31-35
    • Knowles, D.1
  • 56
    • 0035071607 scopus 로고    scopus 로고
    • A small molecule designed to bind to the adenine nucleotide pocket of Hsp90 causes Her2 degradation and the growth arrest and differentiation of breast cancer cells
    • Chiosis, G.; Timaul, M. N.; Lucas, B.; Munster, P. N.; Zheng, F. F.; Sepp-Lorenzino, L.; Rosen, N. A small molecule designed to bind to the adenine nucleotide pocket of Hsp90 causes Her2 degradation and the growth arrest and differentiation of breast cancer cells. Chem. Biol. 2001, 8, 289-299.
    • (2001) Chem. Biol. , vol.8 , pp. 289-299
    • Chiosis, G.1    Timaul, M.N.2    Lucas, B.3    Munster, P.N.4    Zheng, F.F.5    Sepp-Lorenzino, L.6    Rosen, N.7
  • 58
    • 21244479038 scopus 로고    scopus 로고
    • Preparation of 3,4-diarylpyrazoles as inhibitors of heat shock protein 90 (HSP90) and their use in the therapy of cancer. WO 03/055860, 2003
    • Drysdale, M. J.; Dymock, B. W.; Barril-Alonso, X.; Workman, P.; Pearl, L. H.; Promodrou, C.; MacDonald, E. Preparation of 3,4-diarylpyrazoles as inhibitors of heat shock protein 90 (HSP90) and their use in the therapy of cancer. WO 03/055860, 2003.
    • Drysdale, M.J.1    Dymock, B.W.2    Barril-Alonso, X.3    Workman, P.4    Pearl, L.H.5    Promodrou, C.6    MacDonald, E.7
  • 63
    • 0036280661 scopus 로고    scopus 로고
    • Ligand binding affinities from MD simulations
    • Aqvist, J.; Luzhkov, V. B.; Brandsdal, B. O. Ligand binding affinities from MD simulations. Acc. Chem. Res. 2002, 35, 358-365.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 358-365
    • Aqvist, J.1    Luzhkov, V.B.2    Brandsdal, B.O.3
  • 64
    • 4043058000 scopus 로고    scopus 로고
    • Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock
    • Morley, S. D.; Afshar, M. Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock. J. Comput.-Aided Mol. Des 2004, 18, 189-208.
    • (2004) J. Comput.-Aided Mol. Des. , vol.18 , pp. 189-208
    • Morley, S.D.1    Afshar, M.2
  • 65
    • 84988115618 scopus 로고
    • Validation of the General Purpose Tripos 5.2 Force Field
    • Clark, M.; Cramer, R. D., III; Van Opdenbosch, N. Validation of the General Purpose Tripos 5.2 Force Field. J. Comput. Chem. 1989, 10, 982-1012.
    • (1989) J. Comput. Chem. , vol.10 , pp. 982-1012
    • Clark, M.1    Cramer III, R.D.2    Van Opdenbosch, N.3


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