Pharmacophoric pattern matching in files of three-dimensional chemical structures: use of bounded distance matrices for the representation and searching of conformationally flexible molecules
Tài liệu tham khảo
Barnard, 1989, Recent developments in chemical structure handling, Perspectives in Information Management, 1, 133
Lipscombe, 1989, Chemical structure processing, Ann. Rev. Inf. Sci. Technol., 24, 189
Cohen, 1990, Molecular modeling software and methods for medicinal chemistry, J. Med. Chem., 33, 883, 10.1021/jm00165a001
Gund, 12171973, Computer searching of a molecular structure for pharmacophoric patterns, 33
Gund, 1977, Three-dimensional pharmacophoric pattern searching, Progress in Molecular and Subcellular Biol., 5, 117, 10.1007/978-3-642-66626-1_4
Brint, 1987, Pharmacophoric pattern matching in files of three-dimensional chemical structures: comparison of geometric searching algorithms, J. Mol. Graphics, 5, 49, 10.1016/0263-7855(87)80045-0
Jakes, 1986, Pharmacophoric pattern matching in files of three-dimensional chemical structures: selection of interatomic distance screens, J. Mol. Graphics, 4, 12, 10.1016/0263-7855(86)80088-1
Cringean, 1990, Selection of screens for three-dimensional substructure searching, Tetrahedron Comp. Method., 3, 37, 10.1016/0898-5529(90)90119-S
Poirrette, 1991, Pharmacophoric pattern matching in files of 3-D chemical structures: characterization and use of generalized valence angle screens, J. Mol. Graphics, 9, 203, 10.1016/0263-7855(91)80013-P
Jakes, 1987, Pharmacophoric pattern matching in files of three-dimensional chemical structures: evaluation of search performance, J. Mol. Graphics, 5, 41, 10.1016/0263-7855(87)80044-9
Bawden, 1988, Development of the Pfizer integrated research data system SOCRATES, 63
Rusinko, 1989, Using CONCORD to construct a large database of three-dimensional coordinates from connection tables, J. Chem. Inf. Comp. Sci., 29, 251, 10.1021/ci00064a004
Sheridan, 1989, 3DSEARCH: a system for three-dimensional substructure searching, J. Chem. Inf. Comp. Sci., 29, 255, 10.1021/ci00064a005
Christie, 1990, MACCS-3D: a tool for three-dimensional drug design, 137
Murrall, 1990, Conformational freedom in 3-D databases. I. Techniques, J. Chem. Inf. Comp. Sci., 30, 312, 10.1021/ci00067a016
Davies, 1990, Performance characteristics in 3-D database searching, 129
Van, 1989, ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure search of 3D molecular structures., J. Comp.-Aided Mol. Design, 3, 225, 10.1007/BF01533070
Martin, 1990, Computer design of potentially bioactive molecules by geometrie searching with ALADDIN, Tetrahedron Comp. Method., 3, 15, 10.1016/0898-5529(90)90117-Q
Bartlett, 1989, CAVEAT: a program to facilitate the structure-derived design of biologically active molecules, 182
Martin, 1990, Searching databases of three-dimensional structures, 213
Willett, 1991
1989
Crippen, 1979, Distance geometry approach to rationalizing binding data, J. Med. Chem., 22, 988, 10.1021/jm00194a020
Behling, 1988, Conformation of acetylcholine bound to the nicotinic acetylcholine receptor, Proc. Nat. Acad. Sci. USA, 85, 6721, 10.1073/pnas.85.18.6721
Haraki, K.S., Sheridan, R.P., Rusinko, A., Venkataraghavan, R., Dunn, D.A. and McCulloch, D. Looking for pharmacophores in 3-D databases: does conformational searching improve the yield of actives? paper presented at the 4th Chemical Congress of North America,New York, 25–30 August 1991
Havel, 1983, The theory and practice of distance geometry, Bull. Math. Biol., 45, 665, 10.1007/BF02460044
Ghose, 1985, Geometrically feasible binding modes of a flexible ligand molecule at the receptor site, J. Comp. Chem., 6, 350, 10.1002/jcc.540060504
Easthope, 1989, Computational experience with an algorithm for tetrangle inequality bound smoothing, Bull. Math. Biol., 51, 173, 10.1007/BF02458843
Clark, 1991, Pharmacophoric pattern matching in files of three-dimensional chemical structures: use of smoothed bounded distances for incompletely specified query patterns, J. Mol. Graphics, 9, 157, 10.1016/0263-7855(91)80003-I
Smellie, 1989, Distance Geometry: New Methods and Applications
Wenger, 1982, Deriving 3D representations of molecular structure from connection tables augmented with configuration designations using distance geometry, J. Chem. Inf. Comp. Sci., 22, 29, 10.1021/ci00033a006
Ullmann, 1976, An algorithm for subgraph isomorphism, J. Assoc. Computing Machinery, 23, 31, 10.1145/321921.321925
Hurst T., private communication
Howard, 1988, An analysis of current methodologies for conformational searching of complex molecules, J. Med. Chem., 31, 1669, 10.1021/jm00117a001
Blaney, J.M., Crippen, G.M. Dearing, A. and Dixon, J.S. DGEOM: distance geometry. Quantum Chemistry Program Exchange program number 590, Department of Chemistry, Indiana University, Bloomington, Indiana, USA
Daylight Chemical Information Systems, 3951 Claremont Street, Irvine, California, USA
Rusinko, 1988
Kuntz, 1989, Distance geometry. Meth. Enzymology, 177, 159, 10.1016/0076-6879(89)77011-7
Dammkoehler, 1989, Constrained search of conformational hyperspace, J. Comp.-Aided Mol. Design, 3, 3, 10.1007/BF01590992
Kier, 1989, An index of molecular flexibility from kappa shape attributes, Quant. Struct.-Act. Relat., 8, 218, 10.1002/qsar.19890080307
Fisanick, W., Cross, K.P. and Rusinko III, A. Characteristics of computer-generated 3D and related molecular property data for CAS Registry substances, paper presented at the 4th Chemical Congress of North America, New York, 25–30 August 1991
Crippen, 1977, A novel approach to the calculation of conformation: distance geometry, J. Comp. Phys., 24, 96, 10.1016/0021-9991(77)90112-7
Havel, 1991, An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance, Prog. Biophys. Mol. Biol., 56, 43, 10.1016/0079-6107(91)90007-F
Bradshaw, J. and Maliski, E.G. Use of most restrictive paths in 3-D search strategy. Paper presented at the 4th Chemical Congress of North America, New York, 25–30 August 1991