BOOMSLANG: a program for combinatorial structure generation.

An approach to exploiting pharmacophore models is described. Structures are assembled combinatorially from user-defined fragments and flexibly overlaid into the reference frame of the pharmacophore using distance geometry and molecular mechanics. The match with the pharmacophore is quantified by conformational energy and volume of overlap.

[1]  Michael L. Connolly,et al.  Computation of molecular volume , 1985 .

[2]  R. Diamond.  A note on the rotational superposition problem , 1988 .

[3]  Chris M. W. Ho,et al.  DBMAKER: A set of programs to generate three-dimensional databases based upon user-specified criteria , 1995, J. Comput. Aided Mol. Des..

[4]  S. P. Fodor,et al.  Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. , 1994, Journal of medicinal chemistry.

[5]  R. Cramer,et al.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.

[6]  Garland R. Marshall,et al.  Constrained search of conformational hyperspace , 1989, J. Comput. Aided Mol. Des..

[7]  Andrew R. Leach,et al.  Current methods for site-directed structure generation , 1994, J. Comput. Aided Mol. Des..

[8]  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..

[9]  G. M. Crippen,et al.  Distance geometry and conformational calculations , 1981 .

[10]  Paul A. Bartlett,et al.  CAVEAT: A program to facilitate the design of organic molecules , 1994, J. Comput. Aided Mol. Des..

[11]  Hans-Joachim Böhm,et al.  The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..

[12]  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..

[13]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[14]  B. Masek,et al.  Molecular shape comparison of angiotensin II receptor antagonists. , 1993, Journal of medicinal chemistry.

[15]  Y. Martin,et al.  3D database searching in drug design. , 1992, Journal of medicinal chemistry.

[16]  S. P. Fodor,et al.  Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. , 1994, Journal of medicinal chemistry.

[17]  G. Jung,et al.  Multiple Peptide Synthesis Methods and Their Applications. New Synthetic Methods (87) , 1992 .

[18]  David Weininger,et al.  CHUCKLES: A method for representing and searching peptide and peptoid sequences on both monomer and atomic levels , 1994, J. Chem. Inf. Comput. Sci..

[19]  Gordon M. Crippen,et al.  Distance Geometry and Molecular Conformation , 1988 .

[20]  Grant D. Green,et al.  Chapter 33. Recent Advances in the Generation of Molecular Diversity , 1993 .

[21]  M. Karplus,et al.  Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. , 1993, Journal of medicinal chemistry.

[22]  M. Murcko,et al.  GroupBuild: a fragment-based method for de novo drug design. , 1993, Journal of medicinal chemistry.

[23]  R. Burch.  Mass ligand binding screening for receptor antagonists: prototype new drugs and blind alleys. , 1991, Journal of receptor research.

[24]  David Weininger,et al.  SMILES. 2. Algorithm for generation of unique SMILES notation , 1989, J. Chem. Inf. Comput. Sci..

[25]  Regine Bohacek,et al.  Multiple Highly Diverse Structures Complementary to Enzyme Binding Sites: Results of Extensive Application of a de Novo Design Method Incorporating Combinatorial Growth , 1994 .