Active-site-directed 3D database searching: Pharmacophore extraction and validation of hits
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David E. Clark | David R. Westhead | Christopher W. Murray | Richard A. Sykes | D. E. Clark | C. Murray | D. Westhead
[1] Julian R. Ullmann,et al. An Algorithm for Subgraph Isomorphism , 1976, J. ACM.
[2] Elaine C. Meng,et al. Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities , 1994, J. Comput. Aided Mol. Des..
[3] Tad Hurst,et al. Flexible 3D searching: The directed tweak technique , 1994, J. Chem. Inf. Comput. Sci..
[4] Andrew S. Glassner,et al. Graphics Gems , 1990 .
[5] Robert P. Sheridan,et al. 3DSEARCH: a system for three-dimensional substructure searching , 1989, J. Chem. Inf. Comput. Sci..
[6] Robert C. Glen,et al. A genetic algorithm for the automated generation of molecules within constraints , 1995, J. Comput. Aided Mol. Des..
[7] N. W. Murrall,et al. How accurate does a force field need to be? , 1989, Comput. Chem..
[8] Hans-Joachim Böhm,et al. On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..
[9] David Bawden,et al. Pharmacophoric pattern matching in files of 3d chemical structures: evaluation of search performance , 1987 .
[10] Ralph E. Christoffersen,et al. Computer-assisted drug design , 1979 .
[11] M. Lawrence,et al. CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure , 1992, Proteins.
[12] Peter Willett,et al. Similarity Searching in Files of Three-Dimensional Chemical Structures. Alignment of Molecular Electrostatic Potential Fields with a Genetic Algorithm , 1996, J. Chem. Inf. Comput. Sci..
[13] Gareth Jones,et al. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation , 1995, J. Comput. Aided Mol. Des..
[14] I. Kuntz,et al. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. , 1988, Journal of medicinal chemistry.
[15] Garland R. Marshall,et al. Sampling conformational hyperspace: Techniques for improving completeness , 1995, J. Comput. Aided Mol. Des..
[16] D. Banner,et al. Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors. , 1994, The Journal of biological chemistry.
[17] A. Ghose,et al. Determination of Pharmacophoric Geometry for Collagenase Inhibitors Using a Novel Computational Method and Its Verification Using Molecular Dynamics, NMR, and X-ray Crystallography , 1995 .
[18] R. Sheridan,et al. The ensemble approach to distance geometry: application to the nicotinic pharmacophore. , 1986, Journal of medicinal chemistry.
[19] J. Gasteiger,et al. ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .
[20] Robert P. Sheridan,et al. FLOG: A system to select ‘quasi-flexible’ ligands complementary to a receptor of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..
[21] T Honma,et al. Novel angiotensin II receptor antagonists. Design, synthesis, and in vitro evaluation of dibenzo[a,d]cycloheptene and dibenzo[b,f]oxepin derivatives. Searching for bioisosteres of biphenylyltetrazole using a three-dimensional search technique. , 1995, Journal of medicinal chemistry.
[22] Arthur Dalby,et al. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited , 1992, J. Chem. Inf. Comput. Sci..
[23] M. Walkinshaw. Protein targets for structure‐based drug design , 1992, Medicinal research reviews.
[24] J. Gasteiger,et al. FROM ATOMS AND BONDS TO THREE-DIMENSIONAL ATOMIC COORDINATES : AUTOMATIC MODEL BUILDERS , 1993 .
[25] Garland R. Marshall,et al. The Conformational Parameter in Drug Design: The Active Analog Approach , 1979 .
[26] P. Grootenhuis,et al. Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes. , 1995, Acta crystallographica. Section D, Biological crystallography.
[27] Peter Willett,et al. Pharmacophoric pattern matching in files of 3-D chemical structures: election of interatomic distance screens , 1986 .
[28] Peter Willett,et al. Similarity Searching in Files of Three-Dimensional Chemical Structures: Flexible Field-Based Searching of Molecular Electrostatic Potentials , 1996, J. Chem. Inf. Comput. Sci..
[29] PatrickY.-S. Lam,et al. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. , 1994, Science.
[30] I. Kuntz,et al. Matching chemistry and shape in molecular docking. , 1993, Protein engineering.
[31] Thomas E. Moock,et al. Conformational searching in ISIS/3D databases , 1994, J. Chem. Inf. Comput. Sci..
[32] David Weininger,et al. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..
[33] Daniel A. Gschwend,et al. Orientational sampling and rigid‐body minimization in molecular docking , 1993, Proteins.
[34] Garland R. Marshall,et al. Constrained search of conformational hyperspace , 1989, J. Comput. Aided Mol. Des..
[35] Mark Whittaker,et al. A Monte Carlo pharmacophore generation procedure: Application to the human PAF receptor , 1993, J. Comput. Aided Mol. Des..
[36] M. Hahn. Receptor surface models. 1. Definition and construction. , 1995, Journal of medicinal chemistry.
[37] M Karplus,et al. Functionality map analysis of the active site cleft of human thrombin , 1996, J. Comput. Aided Mol. Des..
[38] Yvonne C. Martin,et al. ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures , 1989, J. Comput. Aided Mol. Des..
[39] Barry Robson,et al. PRO_LIGAND: An approach to de novo molecular design. 1. Application to the design of organic molecules , 1995, J. Comput. Aided Mol. Des..
[40] Gerhard Klebe,et al. Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures , 1994, J. Chem. Inf. Comput. Sci..
[41] Hans-Joachim Böhm,et al. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads , 1992, J. Comput. Aided Mol. Des..
[42] David E. Clark,et al. PRO_LIGAND: An approach to de novo molecular design. 6. Flexible fitting in the design of peptides , 1995, J. Comput. Aided Mol. Des..
[43] David E. Clark,et al. MOLMAKER: De Novo Generation of 3D Databases for Use in Drug Design , 1996, J. Chem. Inf. Comput. Sci..
[44] John Bradshaw,et al. Comparison of conformations of small molecule structures from the Protein Data Bank with those generated by Concord, Cobra, ChemDBS-3D, and Converter and those extracted from the Cambridge Structural Database , 1993, J. Chem. Inf. Comput. Sci..
[45] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[46] I. Kuntz,et al. Structure-based discovery of inhibitors of thymidylate synthase. , 1993, Science.
[47] Dorica Mayer,et al. A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies , 1987, J. Comput. Aided Mol. Des..
[48] Yvonne C. Martin,et al. A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists , 1993, J. Comput. Aided Mol. Des..
[49] G. Claeson,et al. In vitro and in vivo characterization of a neutral boron-containing thrombin inhibitor. , 1993, The Journal of biological chemistry.
[50] Y. Martin,et al. 3D database searching in drug design. , 1992, Journal of medicinal chemistry.
[51] Peter Willett,et al. Similarity Searching in Files of Three-Dimensional Structures: Evaluation of Similarity Coefficients and Standardisation Methods for Field-Based Similarity Searching , 1995 .
[52] Jack Ritter,et al. An efficient bounding sphere , 1990 .
[53] C. R. Watts,et al. Rationally Designed N,N’-Bis[(N-p-guanidinobenzyl-N-methyl)aminocarbonyl]-1,3-diaminobenzene, “BIGBEN”, Binds to the Minor Groove of d(CGCGAATTCGCG)2 as Determined by Two-Dimensional Nuclear Magnetic Resonance Spectroscopy , 1995 .
[54] N. W. Murrall,et al. Conformational freedom in 3-D databases. 1. Techniques , 1990, J. Chem. Inf. Comput. Sci..
[55] P. Willett,et al. Pharmacophoric pattern matching in files of 3d chemical structures: comparison of geometric searching algorithms , 1987 .
[56] I. Kuntz,et al. Automated docking with grid‐based energy evaluation , 1992 .
[57] Ajay,et al. Computational methods to predict binding free energy in ligand-receptor complexes. , 1995, Journal of medicinal chemistry.
[58] I. Kuntz. Structure-Based Strategies for Drug Design and Discovery , 1992, Science.
[59] F E Cohen,et al. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[60] P. Willett,et al. Searching Techniques for Databases of Three-Dimensional Chemical Structures. , 1994 .
[61] D W Zaharevitz,et al. The discovery of novel, structurally diverse protein kinase C agonists through computer 3D-database pharmacophore search. Molecular modeling studies. , 1994, Journal of medicinal chemistry.
[62] Shaomeng Wang,et al. Estimation of aqueous solubility of organic molecules by the group contribution approach. Application to the study of biodegradation , 1992, J. Chem. Inf. Comput. Sci..
[63] Hans-Joachim Böhm,et al. The computer program LUDI: A new method for the de novo design of enzyme inhibitors , 1992, J. Comput. Aided Mol. Des..
[64] P. Gund. Three-Dimensional Pharmacophoric Pattern Searching , 1977 .
[65] George W. A. Milne,et al. CONCORD and CAMBRIDGE: comparison of computer generated chemical structures with x-ray crystallographic data , 1993, J. Chem. Inf. Comput. Sci..
[66] Andrew Smellie,et al. Identification of Common Functional Configurations Among Molecules , 1996, J. Chem. Inf. Comput. Sci..
[67] G. Klebe. The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands. , 1994, Journal of molecular biology.
[68] F. Diederich,et al. Design of Novel, Nonpeptidic Thrombin Inhibitors and Structure of a Thrombin–Inhibitor Complex , 1995 .
[69] A. Sykes,et al. Hexaaquatitanium(III) Tris(p-Toluenesulfonate) Trihydrate , 1995 .
[70] Arup K. Ghose,et al. Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics , 1989, J. Chem. Inf. Comput. Sci..
[71] P Willett,et al. Pharmacophoric pattern matching in files of three-dimensional chemical structures: use of bounded distance matrices for the representation and searching of conformationally flexible molecules. , 1992, Journal of molecular graphics.
[72] Gareth Jones,et al. Pharmacophoric pattern matching in files of three-dimensional chemical structures: Comparison of conformational-searching algorithms for flexible searching , 1994, J. Chem. Inf. Comput. Sci..
[73] Peter Willett,et al. Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances , 1991, J. Comput. Aided Mol. Des..