Molecular field technology applied to virtual screening and finding the bioactive conformation

Bibliography

• CHEESERIGHT T, MACKEY M, ROSE S, VINTER A: Molecular field extrema as descriptors of biological activity: definition and validation. J. Chem. Inf. Model. (2006) 46:665-676.
   PubMed Web of Science ®Google Scholar
• CHEESERIGHT T, MACKEY M, VINTER JG: Peptides to non-peptides: leads from structureless virtual screening. Drug Discov. Today (2004) 2:57-60.
   Google Scholar
• AJAY N: Virtual screening in lead discovery and optimization. Curr. Opin. Lead Disc. Dev. (2004) 7:396-404.
   PubMed Web of Science ®Google Scholar
• LENGAUER T, LEMMEN C, RAREY M, ZIMMERMANN M: Novel technologies for virtual screening. Drug Discov. Today (2004) 9:27-34.
   PubMed Web of Science ®Google Scholar
• OPREA TI, MATTER H: Integrating virtual screening in lead discovery. Curr. Opin. Chem. Biol. (2004) 8:349-358.
   PubMed Web of Science ®Google Scholar
• KITCHEN DB, DECORNEZ H, FURR JR, BAJORATH J: Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Disc. (2004) 11:935-949.
   Web of Science ®Google Scholar
• VERDONK ML, COLE JC, HARTSHORN M, MURRAY C, TAYLOR RD: Improved protein-ligand docking using GOLD. Proteins (2003) 52:609-623.
   PubMed Web of Science ®Google Scholar
• PEROLA E, WALTERS WP, CHARIFSON PS: A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins (2004) 56:235-249.
   PubMed Web of Science ®Google Scholar
• WILLETT P: Chemical similarity searching. J. Chem. Inf. Comp. Sci. (1998) 38:983-996.
   Google Scholar
• PATEL Y, GILLET VJ, BRAVI G, LEACH AR: A comparison of the pharmacophore identification programs Catalyst, DISCO and GASP. J. Comp.-Aid. Mol. Des. (2002) 16:653-681.
   PubMed Web of Science ®Google Scholar
• LANGER T, HOFFMAN RD: Pharmacophores and Pharmacophore Searches, in the Methods and Principles in Medicinal Chemistry Series. Vol. 32, Mannhold R, Kubinyi H, Folkers G (Eds), Wiley VCH, Weinheim (2006).
   Google Scholar
• WOLBER G, LANGER T: Ligandscout: 3D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model. (2005) 45:160-169.
   PubMed Web of Science ®Google Scholar
• DAVIS A, WARRINGTON B, VINTER JG: Strategies in drug design II- modelling studies on phosphodiesterase substrates and inhibitors. J. Comp-Aid. Mol. Des. (1987) 1:97-120.
   PubMedGoogle Scholar
• VINTER JG, SAUNDERS MR: Molecular modelling approaches to host-guest complexes. In: Host-Guest Molecular Interactions: from Chemistry to Biology, Ciba Foundation Symposium No 158, Wiley (1991):249-261.
   Google Scholar
• APAYA RP, LUCCHESE B, PRICE SL, VINTER JG: The matching of electrostatic extrema: a useful method in drug design? A study of phosphodiesterase III inhibitors. J. Comp-Aid. Mol. Des. (1995) 9:33-43.
   PubMed Web of Science ®Google Scholar
• VINTER JG, TROLLOPE KI: Multi-conformational composite molecular fields in the analysis of drug design. (1) Methodology and first evaluation using 5HT and histamine action as examples. J. Comp-Aid. Mol. Des. (1995) 9:297-307.
   PubMed Web of Science ®Google Scholar
• HUNTER CA, SANDERS JKM: The nature of π–π interactions. J. Am. Chem. Soc. (1990) 112:5525-5534.
   Web of Science ®Google Scholar
• VINTER JG: Extended electron distributions applied to the molecular mechanics of intermolecular interactions. J. Comp-Aid. Mol. Des. (1994) 8:653-668.
   PubMed Web of Science ®Google Scholar
• VINTER JG: Extended electron distributions applied to the molecular mechanics of intermolecular interactions. II-Organic complexes. J. Comp-Aid. Mol. Des. (1996) 10:417-426.
   PubMed Web of Science ®Google Scholar
• STONE AJ, PRICE SL: Some new ideas in the theory of intermolecular forces: anisotropic atom-atom potentials. J. Phys. Chem. (1988) 92:3325-3335.
   Web of Science ®Google Scholar
• LOZMAN OR, BUSHBY RJ, VINTER JG: Complementary polytopic interactions (CPI) as revealed by molecular modelling using the XED force field. J. Chem. Soc. Perkin (2001) 2:1446-1453.
   Google Scholar
• CHESSARI G, HUNTER CA, LOW CMR, PACKER MJ, VINTER JG, ZONTA C: An evaluation of force field treatments of aromatic interactions. Chem. Eur. J. (2002) 8:2860-2867.
   PubMed Web of Science ®Google Scholar
• SUZUKI S, GREEN PG, BUMGARNER RE, DASGUPTA S, GODDARD WA, BLAKE GA: Benzene forms hydrogen bonds with water. Science (1992) 257:942-945.
   PubMed Web of Science ®Google Scholar
• DOUGHERTY DA: Cation–pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr and Trp. Science (1996) 271:163-168.
   PubMed Web of Science ®Google Scholar
• LOW CMR, BUCK IM, COOKE T et al.: Scaffold hopping with molecular field points: identification of a cholecystokinin-2 (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.
   PubMed Web of Science ®Google Scholar
• HILLISCH A, PINEDA LF, HILGENFELD R: Utility of homology models in the drug discovery process. Drug Discov. Today (2004) 9:659-669.
   PubMed Web of Science ®Google Scholar
• GREENE J, KAHN S, SAVOJ P, SPRAGUE P, TEIG S: Chemical function queries for 3D database search. J. Chem. Inf. Comput. Sci. (1994) 34:1297-1308.
   Google Scholar
• MASON JS, MORIZE I, MENARD PR, CHENEY DI, HULME C, LABAUDINIERE RF: New 4-point pharmacophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J. Med. Chem. (1999) 42:3251-3264.
   PubMed Web of Science ®Google Scholar
• CRAMER RD, PATTERSON DE, BUNCE JD: Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. (1988) 110:5959-5967.
   PubMed Web of Science ®Google Scholar
• GOODFORD PJ: A computational procedure for determining energetically favourable binding sites on biologically important macromolecules. J. Med. Chem. (1985) 28:849-857.
   PubMed Web of Science ®Google Scholar
• BARONI M, COSTANTINO G, CRUCIANI G, RIGANELLI D, VALIGI R, CLEMENTI S: Generating optimal linear PLS estimations (GOLPE); an advanced chemometric tool for handling 3D-QSAR problems. Quant. Struct.-Act. Relat. (1993) 12:9-20.
   Web of Science ®Google Scholar
• CRUCIANI G, MENICONI M, CAROSATI E, ZAMORA I, MANNHOLD R: VOLSURF: A Tool for Drug ADME-properties Prediction. In: Drug Bioavailability. Estimation of Solubility, Permeability and Absorption, Methods and Principles in Medicinal Chemistry (volume 18). Van de Waterbeemd H, Lennernäs H, Artursson P (Eds.), Wiley-VCH, Weinheim (2003):406-419.
   Google Scholar
• PASTOR M, CRUCIANI G, MCLAY I, PICKETT S, CLEMENTI S: GRID-independent descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors. J. Med. Chem. (2000) 43:3233-3243.
   PubMed Web of Science ®Google Scholar
• CRUCIANI G, ARISTEI Y, VIANELLO R, BARONI M: GRID-derived molecular interaction fields for predicting the site of metabolism in human cytochromes. In: Molecular Interaction Fields, Cruciani G (Ed), in the Methods and Principles in Medicinal Chemistry Series Vol. 32, Mannhold R, Kubinyi H, Folkers G (Eds), Wiley-VCH, Weinheim (2006):273-290.
   Google Scholar