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Volumn 46, Issue 8, 2003, Pages 1359-1371

Field interaction and geometrical overlap: A new simplex and experimental design based computational procedure for superposing small ligand molecules

Author keywords

[No Author keywords available]

Indexed keywords

DRUG; LIGAND;

EID: 0037431383     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm0210616     Document Type: Article
Times cited : (39)

References (47)
  • 1
    • 0037061635 scopus 로고    scopus 로고
    • GBR compounds mepyramines as cocaine abuse therapeutics chemometric studies on selectivity using grid independent descriptors (GRIND)
    • Benedetti, P.; Mannhold, R.; Cruciani, G.; Pastor, M. GBR Compounds and Mepyramines as Cocaine Abuse Therapeutics: Chemometric Studies on Selectivity Using Grid Independent Descriptors (GRIND). J. Med. Chem. 2002, 45, 1577-1584.
    • (2002) J. Med. Chem. , vol.45 , pp. 1577-1584
    • Benedetti, P.1    Mannhold, R.2    Cruciani, G.3    Pastor, M.4
  • 2
    • 0242474469 scopus 로고    scopus 로고
    • Grid independent descriptors (GRIND) in the study of σ-receptor subtype selectivity
    • Gratteri, P.; Romanelli, M. N.; Bonaccini, C. Grid independent descriptors (GRIND) in the study of σ-receptor subtype selectivity. Drugs Future 2002, 27 (Suppl. A), 257.
    • (2002) Drugs Future , vol.27 , Issue.SUPPL. A , pp. 257
    • Gratteri, P.1    Romanelli, M.N.2    Bonaccini, C.3
  • 3
    • 0242474464 scopus 로고    scopus 로고
    • Incorporating shape into the grid-independent descriptors: Applications in 3D-QSAR and bioactive conformation searching
    • Fontaine, F.; Pastor, M.; Sanz, F. Incorporating Shape into the Grid-INdependent Descriptors: Applications in 3D-QSAR and Bioactive Conformation Searching. Drugs Future 2002, 27 (Suppl. A), 232.
    • (2002) Drugs Future , vol.27 , Issue.SUPPL. A , pp. 232
    • Fontaine, F.1    Pastor, M.2    Sanz, F.3
  • 5
    • 0034710718 scopus 로고    scopus 로고
    • Grid independent descriptors (GRIND). A novel class of alignment-independent three-dimensional descriptors
    • Pastor, M.; Cruciani, G.; McLay, I.; Pickett, S.; Clementi, S. Grid Independent Descriptors (GRIND). A Novel Class of Alignment-Independent Three-Dimensional Descriptors. J. Med. Chem. 2000, 43, 3233-3242.
    • (2000) J. Med. Chem. , vol.43 , pp. 3233-3242
    • Pastor, M.1    Cruciani, G.2    McLay, I.3    Pickett, S.4    Clementi, S.5
  • 6
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-857.
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 7
    • 0003521340 scopus 로고    scopus 로고
    • Molecular Discovery Ltd. (20 A Bearkeley Street): Mayfair, London, England
    • GRID, version 19; Molecular Discovery Ltd. (20 A Bearkeley Street): Mayfair, London, England, 2001.
    • (2001) GRID, Version 19
  • 8
    • 0000532443 scopus 로고    scopus 로고
    • Use of the supermolecule approach to derive molecular similarity descriptors for QSAR analysis
    • Cocchi, M.; De Benedetti, P. G. Use of the Supermolecule Approach To Derive Molecular Similarity Descriptors for QSAR Analysis. J. Mol. Model. 1998, 4, 113-131.
    • (1998) J. Mol. Model. , vol.4 , pp. 113-131
    • Cocchi, M.1    De Benedetti, P.G.2
  • 9
    • 0242642878 scopus 로고    scopus 로고
    • Discrete pattern recognition by fitting onto a continuous function
    • Cossé-Barbi, A.; Raji, M. Discrete pattern recognition by fitting onto a continuous function. J. Comput. Chem. 1997, 18, 1875-1892.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1875-1892
    • Cossé-Barbi, A.1    Raji, M.2
  • 11
    • 0032568091 scopus 로고    scopus 로고
    • A new method for predicting the alignment of flexible molecules orienting them in a receptor cleft of known structure
    • De Rosa, M. C.; Berglund, A. A New Method for Predicting the Alignment of Flexible Molecules and Orienting Them in a Receptor Cleft of Known Structure. J. Med. Chem. 1998, 41, 691-698.
    • (1998) J. Med. Chem. , vol.41 , pp. 691-698
    • De Rosa, M.C.1    Berglund, A.2
  • 12
    • 0001458213 scopus 로고
    • The utilization of gaussian functions for the rapid evaluation of molecular similarity
    • Good, A. C.; Hodgkin, E. E.; Richards, W. G. The Utilization of Gaussian Functions for the Rapid Evaluation of Molecular Similarity. J. Chem. Inf. Comput. Sci. 1992, 32, 188-191.
    • (1992) J. Chem. Inf. Comput. Sci. , vol.32 , pp. 188-191
    • Good, A.C.1    Hodgkin, E.E.2    Richards, W.G.3
  • 13
    • 0001109246 scopus 로고    scopus 로고
    • A fast method of molecular shape comparison a simple application of a gaussian description of molecular shape
    • Grant, J. A.; Gallardo, M. A.; Pickup, B. T. A Fast Method of Molecular Shape Comparison: A Simple Application of a Gaussian Description of Molecular Shape. J. Comput. Chem. 1996, 17, 1653-1666.
    • (1996) J. Comput. Chem. , vol.17 , pp. 1653-1666
    • Grant, J.A.1    Gallardo, M.A.2    Pickup, B.T.3
  • 14
    • 0032015039 scopus 로고    scopus 로고
    • Superposition of three-dimensional chemical structures allowing for conformational flexibility by a hybrid method
    • Handschuh, S.; Wagener, M.; Gasteiger, J. Superposition of Three-Dimensional Chemical Structures Allowing for Conformational Flexibility by a Hybrid Method. J. Chem. Inf. Comput. Sci. 1998, 38, 220-232.
    • (1998) J. Chem. Inf. Comput. Sci. , vol.38 , pp. 220-232
    • Handschuh, S.1    Wagener, M.2    Gasteiger, J.3
  • 17
    • 0029444383 scopus 로고
    • A genetic algorithm for flexible molecular overlay pharmacophore elucidation
    • Jones, G.; Willet, P.; Glen, R. C. A Genetic Algorithm for Flexible Molecular Overlay and Pharmacophore Elucidation. J. Comput.-Aided Mol. Des. 1995, 9, 532-549.
    • (1995) J. Comput.-Aided Mol. Des. , vol.9 , pp. 532-549
    • Jones, G.1    Willet, P.2    Glen, R.C.3
  • 18
    • 44949267284 scopus 로고
    • An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap
    • Kearsley, S. K.; Smith, G. M. An Alternative Method for the Alignment of Molecular Structures: Maximizing Electrostatic and Steric Overlap. Tetrahedron Comput. Methodol. 1990, 3, 615-633.
    • (1990) Tetrahedron Comput. Methodol. , vol.3 , pp. 615-633
    • Kearsley, S.K.1    Smith, G.M.2
  • 19
    • 0033020898 scopus 로고    scopus 로고
    • Methodological developments and strategies for a fast flexible superposition of drug-size molecules
    • Klebe, G.; Mietzner, T.; Weber, F. Methodological developments and strategies for a fast flexible superposition of drug-size molecules. J. Comput.-Aided Mol. Des. 1999, 13, 35-49.
    • (1999) J. Comput.-Aided Mol. Des. , vol.13 , pp. 35-49
    • Klebe, G.1    Mietzner, T.2    Weber, F.3
  • 20
    • 0032153072 scopus 로고    scopus 로고
    • RigFit: A new approach to superimposing ligand molecules
    • Lemmen, C.; Hiller, C.; Lengauer, T. RigFit: A new approach to superimposing ligand molecules. J. Comput.-Aided Mol. Des. 1998, 12, 491-502.
    • (1998) J. Comput.-Aided Mol. Des. , vol.12 , pp. 491-502
    • Lemmen, C.1    Hiller, C.2    Lengauer, T.3
  • 21
    • 0031183511 scopus 로고    scopus 로고
    • Time-efficient flexible superposition of medium-sized molecules
    • Lemmen, C.; Lengauer, T. Time-efficient flexible superposition of medium-sized molecules J. Comput.-Aided Mol. Des. 1997, 11, 357-368.
    • (1997) J. Comput.-Aided Mol. Des. , vol.11 , pp. 357-368
    • Lemmen, C.1    Lengauer, T.2
  • 22
    • 0027548454 scopus 로고
    • A fast new approach to pharmacophore mapping and its applications to dopaminergic and benzodiazepine agonist
    • Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. A fast new approach to pharmacophore mapping and its applications to dopaminergic and benzodiazepine agonist. J. Comput.-Aided Mol. Des. 1993, 7, 83-102.
    • (1993) J. Comput.-Aided Mol. Des. , vol.7 , pp. 83-102
    • Martin, Y.C.1    Bures, M.G.2    Danaher, E.A.3    DeLazzer, J.4    Lico, I.5    Pavlik, P.A.6
  • 23
    • 0027212858 scopus 로고
    • Molecular shape comparison of angiotensin II receptor antagonists
    • Masek, B. B.; Merchant, A.; Matthew, J. R. Molecular Shape Comparison of Angiotensin II Receptor Antagonists. J. Med. Chem. 1993, 36, 1230-1238.
    • (1993) J. Med. Chem. , vol.36 , pp. 1230-1238
    • Masek, B.B.1    Merchant, A.2    Matthew, J.R.3
  • 24
    • 0000358516 scopus 로고    scopus 로고
    • Optimization of carbó molecular similarity index using gradient methods
    • McMahon, A. J.; King, P. M. Optimization of Carbó molecular similarity index using gradient methods. J. Comput. Chem. 1997, 18, 151-158.
    • (1997) J. Comput. Chem. , vol.18 , pp. 151-158
    • McMahon, A.J.1    King, P.M.2
  • 25
    • 0029320502 scopus 로고
    • Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: Comparison of predicted and experimental conformations of inhibitors of three enzymes
    • McMartin, C.; Bohacek, R. S. Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: Comparison of predicted and experimental conformations of inhibitors of three enzymes. J. Comput.-Aided Mol. Des. 1995, 9, 237-250.
    • (1995) J. Comput.-Aided Mol. Des. , vol.9 , pp. 237-250
    • McMartin, C.1    Bohacek, R.S.2
  • 26
    • 0001171748 scopus 로고    scopus 로고
    • MIMIC: A molecular-field matching program. Exploiting applicability of molecular similarity approaches
    • Mestres, J.; Rohrer, D. C.; Maggiora, G. M. MIMIC: A Molecular-Field Matching Program. Exploiting Applicability of Molecular Similarity Approaches. J. Comput. Chem. 1997, 18, 934-954.
    • (1997) J. Comput. Chem. , vol.18 , pp. 934-954
    • Mestres, J.1    Rohrer, D.C.2    Maggiora, G.M.3
  • 27
    • 0033529045 scopus 로고    scopus 로고
    • SQ: A program for rapidly producing pharmacophorically relevent molecular superpositions
    • Miller, M. D.; Sheridan, R. P.; Kearsley, S. K. SQ: A Program for Rapidly Producing Pharmacophorically Relevent Molecular Superpositions. J. Med. Chem. 1999, 42, 1505-1514.
    • (1999) J. Med. Chem. , vol.42 , pp. 1505-1514
    • Miller, M.D.1    Sheridan, R.P.2    Kearsley, S.K.3
  • 28
    • 0000905113 scopus 로고    scopus 로고
    • Superposition of molecules: Electron density fitting by application of Fourier transforms
    • Nissink, J. W. M.; Verdonk, M. L.; Kroon, J.; Nietsner, T.; Klebe, G. Superposition of molecules: Electron density fitting by application of Fourier transforms. J. Comput. Chem. 1997, 18, 638-645.
    • (1997) J. Comput. Chem. , vol.18 , pp. 638-645
    • Nissink, J.W.M.1    Verdonk, M.L.2    Kroon, J.3    Nietsner, T.4    Klebe, G.5
  • 29
    • 0001677264 scopus 로고    scopus 로고
    • Alignment of molecules by the Monte Carlo optimization of molecular similarity indices
    • Parretti, M. F.; Kroemer, R. T.; Rothman, J. H.; Richards, W. G. Alignment of molecules by the Monte Carlo optimization of molecular similarity indices. J. Comput. Chem. 1997, 18, 1344-1353.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1344-1353
    • Parretti, M.F.1    Kroemer, R.T.2    Rothman, J.H.3    Richards, W.G.4
  • 30
    • 0029440003 scopus 로고
    • Molecular surface-volume and property matching to superpose flexible dissimilar molecules
    • Perkins, T. D. J.; Mills, J. E. J.; Dean, P. N. Molecular surface-volume and property matching to superpose flexible dissimilar molecules. J. Comput.-Aided Mol. Des. 1995, 9, 479-490.
    • (1995) J. Comput.-Aided Mol. Des. , vol.9 , pp. 479-490
    • Perkins, T.D.J.1    Mills, J.E.J.2    Dean, P.N.3
  • 31
    • 84986437272 scopus 로고
    • Geometric molecular similarity from volume-based distance minimization: Application to saxitonin and tetrodotoxin
    • Petitjean, M. Geometric Molecular Similarity from Volume-Based Distance Minimization: Application to Saxitonin and Tetrodotoxin. J. Comput. Chem. 1995, 16, 80-90.
    • (1995) J. Comput. Chem. , vol.16 , pp. 80-90
    • Petitjean, M.1
  • 32
    • 0033828444 scopus 로고    scopus 로고
    • MIPSIM: Similarity analysis of molecular interaction potentials
    • de Caceres, M.; Villà, J.; Lozano, J. J.; Sanz, F. MIPSIM: similarity analysis of molecular interaction potentials. Bioinformatics 2000, 16, 568-569.
    • (2000) Bioinformatics , vol.16 , pp. 568-569
    • De Caceres, M.1    Villà, J.2    Lozano, J.J.3    Sanz, F.4
  • 33
    • 0022485091 scopus 로고
    • The ensemble approach to distance geometry: Application to the nicotinic pharmacophore
    • Sheridan, R. P.; Nilakantan, R.; Dixon, J. S.; Venkataraghavan, R. The Ensemble Approach to Distance Geometry: Application to the Nicotinic Pharmacophore. J. Med. Chem. 1986, 29, 899-906.
    • (1986) J. Med. Chem. , vol.29 , pp. 899-906
    • Sheridan, R.P.1    Nilakantan, R.2    Dixon, J.S.3    Venkataraghavan, R.4
  • 34
    • 0034065350 scopus 로고    scopus 로고
    • Computational methods for the structural alignment of molecules
    • Lemmen, C.; Lengauer, T. Computational methods for the structural alignment of molecules. J. Comput.-Aided Mol. Des. 2000, 14, 215-232.
    • (2000) J. Comput.-Aided Mol. Des. , vol.14 , pp. 215-232
    • Lemmen, C.1    Lengauer, T.2
  • 36
    • 0034182176 scopus 로고    scopus 로고
    • Quadratic shape descriptors. 1. Rapid superposition of dissimilar molecules using geometrically invariant surface descriptors
    • Goldmann, B. B.; Wipke, W. T. Quadratic shape descriptors. 1. Rapid superposition of dissimilar molecules using geometrically invariant surface descriptors. J. Chem. Inf. Comput. Sci. 2000, 40, 644-658.
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 644-658
    • Goldmann, B.B.1    Wipke, W.T.2
  • 37
  • 39
    • 0000238336 scopus 로고
    • A simplex method for function minimization
    • Nelder, J. A.; Mead R. A simplex method for function minimization. Comput. J. 1965, 7, 308.
    • (1965) Comput. J. , vol.7 , pp. 308
    • Nelder, J.A.1    Mead, R.2
  • 41
    • 0242558187 scopus 로고    scopus 로고
    • Web site: http://www.biochem.ucl.ac.uk/bsm/pdbsum/.
  • 43
    • 0016061785 scopus 로고
    • An algorithm for the construction of "D-optimal" experimental designs
    • Mitchell, T. J. An Algorithm for the Construction of "D-Optimal" Experimental Designs. Technometrics 1974, 16, 203-210.
    • (1974) Technometrics , vol.16 , pp. 203-210
    • Mitchell, T.J.1
  • 46
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. An All Atom Force Field for Simulations of Proteins and Nucleic Acids. J. Comput. Chem. 1986, 7, 230-252.
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 47
    • 0004247107 scopus 로고    scopus 로고
    • InsightII 2000; Accelrys Inc. (www.accelrys.com).
    • (2000) InsightII 2000


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