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1
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15844389649
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Non-peptide cholecystokinin-B/gastrin receptor antagonists based on bicyclic, heteroaromatic skeletons
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Kalindjian, S. B.; Buck, I. M.; Davies. J. M.; Dunstone, D. J.; Hudson, M. L.; Low, C. M.; McDonald, I. M.; Pether, M. J.; Steel, K. I.; Tozer, M. J.; Vinter, J. G. Non-peptide cholecystokinin-B/gastrin receptor antagonists based on bicyclic, heteroaromatic skeletons. J. Med. Chem. 1996, 39, 1806-1815.
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Kalindjian, S.B.1
Buck, I.M.2
Davies, J.M.3
Dunstone, D.J.4
Hudson, M.L.5
Low, C.M.6
McDonald, I.M.7
Pether, M.J.8
Steel, K.I.9
Tozer, M.J.10
Vinter, J.G.11
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2
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0034699373
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2,7-Dioxo-2,3,4,5,6,7-hexahydro-1H-benzo[h][1,4]diazonine as a new template for the design of CCK(2) receptor antagonists
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McDonald, I. M.; Dunstone, D. J.; Kalindjian, S. B.; Linney, I. D.; Low, C. M.; Pether, M. J.; Steel, K. I.: Tozer, M. J.; Vinter, J. G. 2,7-Dioxo-2,3,4,5,6,7-hexahydro-1H-benzo[h][1,4]diazonine as a new template for the design of CCK(2) receptor antagonists. J. Med. Chem. 2000, 43, 3518-3529.
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McDonald, I.M.1
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Kalindjian, S.B.3
Linney, I.D.4
Low, C.M.5
Pether, M.J.6
Steel, K.I.7
Tozer, M.J.8
Vinter, J.G.9
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3
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27444434546
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Scaffold Hopping with Molecular Field Points: Identification of a CCK2 receptor pharmacophore and its use in the design of a prototypical series of pyrrole- And imidazole-based CCK2 antagonists
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Low, C. M. R.; Buck, I. M.; Cooke, T.; Cushnir, J. R.; Kalindjian, S. B.; Kotecha, A.; Pether, M. J.; Shankley, N. P.; Vinter, J. G.; Wright, L. Scaffold Hopping with Molecular Field Points: identification of a CCK2 receptor pharmacophore and its use in the design of a prototypical series of pyrrole- and imidazole-based CCK2 antagonists. J. Med. Chem. 2005, 48, 6790-6802.
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Low, C.M.R.1
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Cooke, T.3
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Kalindjian, S.B.5
Kotecha, A.6
Pether, M.J.7
Shankley, N.P.8
Vinter, J.G.9
Wright, L.10
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4
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24344484047
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On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimisation approaches for studies of enzymatic reactions
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Klähn, M.; Braun-Sand, S.; Rosta, E.; Warshel, A. On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimisation approaches for studies of enzymatic reactions. J. Phys. Chem. B 2005, 109, 15645-15650.
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Klähn, M.1
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0001227655
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The nature of π - π interactions
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Hunter, C. A.; Sanders, J. K. M. The nature of π - π interactions. J. Am. Chem. Soc. 1990, 112, 5525-5534.
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Hunter, C.A.1
Sanders, J.K.M.2
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0028695270
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Extended electron distributions applied to the molecular mechanics of intermolecular interactions
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Vinter, J. G. Extended electron distributions applied to the molecular mechanics of intermolecular interactions. J. Comput.-Aided Mol. Des. 1994, 8, 653-668.
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Vinter, J.G.1
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7
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0030255292
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Extended electron distributions applied to the molecular mechanics of intermolecular interactions. II-organic complexes
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Vinter, J. G. Extended electron distributions applied to the molecular mechanics of intermolecular interactions. II-Organic Complexes. J. Comput.-Aided Mol. Des. 1996, 10, 417-426.
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Vinter, J.G.1
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8
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0347807962
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Some new ideas in the theory of intermolecular forces: Anisotropic atom-atom potentials
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Stone, A. J.; Price, S. L. Some new ideas in the theory of intermolecular forces: anisotropic atom-atom potentials. J. Phys. Chem. 1988, 92, 3325-3335.
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Stone, A.J.1
Price, S.L.2
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9
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0034741388
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Complementary polytopic interactions (CPI) as revealed by molecular modelling using the XED force field
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Lozman, O. R.; Bushby, R. J.; Vinter, J. G. Complementary polytopic interactions (CPI) as revealed by molecular modelling using the XED force field. J. Chem. Soc., Perkin 2001, 2, 1446-1453.
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Lozman, O.R.1
Bushby, R.J.2
Vinter, J.G.3
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10
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0037007909
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An evaluation of force field treatments of aromatic interactions
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Chessari, G.; Hunter, C. A.; Low, C. M. R.; Packer, M. J.; Vinter, J. G.; Zonta, C. An Evaluation of Force Field Treatments of Aromatic Interactions. Chem. Eur. J. 2002, 8, No. 13, 2860-2867.
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Chessari, G.1
Hunter, C.A.2
Low, C.M.R.3
Packer, M.J.4
Vinter, J.G.5
Zonta, C.6
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11
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0021871375
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A computational procedure for determining energetically favourable binding sites on biologically important macromolecules
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Goodford, P. J. A Computational Procedure for Determining Energetically Favourable Binding Sites on Biologically Important Macromolecules. J. Med. Chem. 1985, 28, 849-857.
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Goodford, P.J.1
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12
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0023751431
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Comparative Molecular Field Analysis (CoMFA) 1. Effect of shape on binding of steroids to carrier proteins
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Cramer, R., D., III.; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA) 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
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Cramer III, R.D.1
Patterson, D.E.2
Bunce, J.D.3
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13
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10844249112
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Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D)
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Bender, A.; Mussa, H. Y.; Gill, G. S.; Glen, R. C. Molecular Surface Point Environments for Virtual Screening and the Elucidation of Binding Patterns (MOLPRINT 3D). J. Med. Chem. 2004, 47, 6569-6583.
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14
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20444385067
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BRUTUS: Optimization of a grid-based similarity function for rigid-body molecular superposition. 1. Alignment and virtual screening applications
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Tervo, A. J.; Ronkko, T.; Nyronen, T. H.; Poso, A. BRUTUS: Optimization of a Grid-Based Similarity Function for Rigid-Body Molecular Superposition. 1. Alignment and Virtual Screening Applications. J. Med. Chem. 2005, 48, 4076-4086.
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Poso, A.4
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15
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0027944195
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Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
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Klebe, G.; Abraham, U.; Mietzner, T. Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological Activity. J. Med. Chem. 1994, 37, 4130-4146.
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Klebe, G.1
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0023380766
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Strategies in drug design II - Modelling studies on phosphodiesterase substrates and inhibitors
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Davis, A.; Warrington, B.; Vinter, J. G. 'Strategies in Drug Design II - Modelling studies on phosphodiesterase substrates and inhibitors'. J. Comput.-Aided Mol. Des. 1987, 1, 97-120.
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Davis, A.1
Warrington, B.2
Vinter, J.G.3
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18
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0029243465
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The matching of electrostatic extrema: A useful method in drug design? A study of phosphodiesterase III inhibitors
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Apaya, R. P.; Lucchese, B.; Price, S. L.; Vinter, J. G. The matching of electrostatic extrema: A useful method in drug design? A study of phosphodiesterase III inhibitors. J. Comput.-Aided Mol. Des. 1995, 9, 33-43.
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Apaya, R.P.1
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Price, S.L.3
Vinter, J.G.4
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19
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0029348108
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Multi-conformational composite molecular fields in the analysis of drug design. (1) Methodology and first evaluation using 5HT and histamine action as examples
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Vinter, J. G.; Trollope, K. I. Multi-conformational Composite Molecular Fields in the Analysis of Drug Design. (1) Methodology and First Evaluation using 5HT and Histamine Action as examples. J. Comput.-Aided Mol. Des. 1995, 9, 297-307.
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Vinter, J.G.1
Trollope, K.I.2
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20
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3342925001
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Peptides to non-peptides: Leads from structureless virtual screening
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Cheeseright, T.; Mackey, M.; Vinter, J. G. Peptides to non-peptides: leads from structureless virtual screening. DDT BIOSILICO 2004, 2, 57-60.
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DDT Biosilico
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Cheeseright, T.1
Mackey, M.2
Vinter, J.G.3
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22
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0000162332
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Benzene forms hydrogen bonds with water
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Suzuki, S.; Green, P. G.; Bumgarner, R. E.; Dasgupta, S.: Goddard, W. A.; Blake, G. A. Benzene Forms Hydrogen Bonds with Water. Science 1992, 257, 942-945.
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Suzuki, S.1
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Dasgupta, S.4
Goddard, W.A.5
Blake, G.A.6
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23
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0030033588
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Cation-pi interactions in chemistry and biology: A new view of benzene, Phe, Tyr and Trp
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Dougherty, D. A. Cation-pi Interactions in Chemistry and Biology: A New View of Benzene, Phe, Tyr and Trp. Science 1996, 271, 163-168.
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Dougherty, D.A.1
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24
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33646229331
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note
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If fields are calculated on a grid constructed around a molecule, their values will change on rotation of the molecule subject to (a) the resolution of the grid and (b) the degree of rotation. This gauge variance must be avoided if molecules are to be optimally overlaid by field comparison. Using a simplex optimization regime for both the generation of field points and the overlaying of field point patterns ensures grid avoidance and gauge invariance.
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25
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0031261930
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A library of information about nonbonded interactions
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Bruno, I. J.; Cole. J. C.; Lommerse, J. P. M.; Rowland, R. S.; Taylor, R.; Verdonk, M. L. Isostar: A library of information about nonbonded interactions. J. Comput.-Aided Mol. Des. 1997, 11, 525-537.
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Bruno, I.J.1
Cole, J.C.2
Lommerse, J.P.M.3
Rowland, R.S.4
Taylor, R.5
Verdonk, M.L.I.6
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26
-
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33646237830
-
-
note
-
When extracting experimental ligand overlays from protein X-ray data, our practice is to overlay all relevant proteins (with their ligands) by least-squares fit on all alpha carbon atoms along all homologous sequences. The procedure is performed graphically, enabling visual judgment to be made of the goodness of fit both of the proteins and ligands. The rare occasions when overlays larger than 0.8 rms were encountered, they were easily recognized as unacceptable and discarded. Having overlaid all relevant proteins, their ligands were isolated by deleting all protein structures and saving the ligands without further coordinate change. The ligand clusters so isolated were subsequently used to calculate the root-mean-square deviation (X-RMS) of our field overlay patterns.
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27
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2342620790
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Roles of conformational and positional adaptability in structure-based design of TMC125 - R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants
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Das, K.; Clark, A. D., Jr.; Lewi, P. J.; Heeres, J.; de Jonge, M. R.; Koymans, L. M. H.; Vinkers, H. M.; Daeyaert, F.; Ludovici, D. W.; Kukla, M. J.; De Corte, B.; Kavash, R. W.; Ho, C. Y.; Ye, H.; Lichtenstein, M. A.; Andries, K.; Pauwels, R.; de Be'thune, M.-P.; Boyer, P. L.; Clark, P.; Hughes, S. H.; Janssen, P. A. J.; Arnold, E. Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125 - R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants. J. Med. Chem. 2004, 47, 2550-2560.
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Das, K.1
Clark Jr., A.D.2
Lewi, P.J.3
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De Jonge, M.R.5
Koymans, L.M.H.6
Vinkers, H.M.7
Daeyaert, F.8
Ludovici, D.W.9
Kukla, M.J.10
De Corte, B.11
Kavash, R.W.12
Ho, C.Y.13
Ye, H.14
Lichtenstein, M.A.15
Andries, K.16
Pauwels, R.17
De Be'thune, M.-P.18
Boyer, P.L.19
Clark, P.20
Hughes, S.H.21
Janssen, P.A.J.22
Arnold, E.23
more..
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28
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0027119143
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Internal stark effect measurement of the electric field at the amino terminus of an alpha helix
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(a) Lockhart D. J.; Kim, P. S. Internal stark effect measurement of the electric field at the amino terminus of an alpha helix. Science 1992, 257, 947-951.
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Science
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Lockhart, D.J.1
Kim, P.S.2
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29
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0027912723
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Electrostatic screening of charge and dipole interactions with the helix backbone
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(b) Lockhart D. J.; Kim, P. S. Electrostatic screening of charge and dipole interactions with the helix backbone. Science 1993, 260, 198-202.
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Lockhart, D.J.1
Kim, P.S.2
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0033057407
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A molecular-field-based similarity study of nonnucleoside HIV-1 reverse transcriptase inhibitors
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(a) Mestres, J.; Rohrer, D. C.; Maggiora, G. M. A molecular-field-based similarity study of nonnucleoside HIV-1 reverse transcriptase inhibitors. J. Comput.-Aided Mol. Des. 1999, 13, 79-93.
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Mestres, J.1
Rohrer, D.C.2
Maggiora, G.M.3
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31
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0033965404
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A molecular-field-based similarity study of nonnucleoside HIV-1 reverse transcriptase inhibitors. 2. the relationship between alignment solutions obtained from conformationally rigid and flexible matching
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(b) Mestres, J.; Rohrer, D. C.; Maggiora, G. M. A molecular-field-based similarity study of nonnucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching. J. Comput.-Aided Mol. Des. 2000. 14, 39-51.
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Mestres, J.1
Rohrer, D.C.2
Maggiora, G.M.3
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