Ligand docking to proteins with discrete side-chain flexibility.

[1]  A. Ghose,et al.  Geometrically feasible binding modes of a flexible ligand molecule at the receptor site , 1985 .

[2]  M. Lawrence,et al.  CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure , 1992, Proteins.

[3]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[4]  Nils J. Nilsson,et al.  A Formal Basis for the Heuristic Determination of Minimum Cost Paths , 1968, IEEE Trans. Syst. Sci. Cybern..

[5]  I. Kuntz,et al.  Structure-based discovery of inhibitors of thymidylate synthase. , 1993, Science.

[6]  C. Sander,et al.  Fast and simple monte carlo algorithm for side chain optimization in proteins: Application to model building by homology , 1992, Proteins.

[7]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[8]  I. Kuntz,et al.  Docking flexible ligands to macromolecular receptors by molecular shape. , 1986, Journal of medicinal chemistry.

[9]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[10]  J. Scott Dixon Flexible docking of ligands to receptor sites using genetic algorithms , 1993 .

[11]  Conrad C. Huang,et al.  The MIDAS display system , 1988 .

[12]  T. L. Blundell,et al.  Knowledge-based prediction of protein structures and the design of novel molecules , 1987, Nature.

[13]  I. Haneef,et al.  A robust and efficient automated docking algorithm for molecular recognition. , 1992, Protein engineering.

[14]  P. Kollman,et al.  An approach to computing electrostatic charges for molecules , 1984 .

[15]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[16]  Randy J. Read,et al.  A multiple‐start Monte Carlo docking method , 1992 .

[17]  I. Kuntz Structure-Based Strategies for Drug Design and Discovery , 1992, Science.

[18]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[19]  G. Cohen,et al.  The three-dimensional structure of a phosphorylcholine-binding mouse immunoglobulin Fab and the nature of the antigen binding site. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[20]  R. Lavery,et al.  A new approach to the rapid determination of protein side chain conformations. , 1991, Journal of biomolecular structure & dynamics.

[21]  W. Bode,et al.  The refined crystal structure of bovine beta-trypsin at 1.8 A resolution. II. Crystallographic refinement, calcium binding site, benzamidine binding site and active site at pH 7.0. , 1975, Journal of molecular biology.

[22]  Nils J. Nilsson,et al.  Principles of Artificial Intelligence , 1980, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[23]  I. Kuntz,et al.  Conformational analysis of flexible ligands in macromolecular receptor sites , 1992 .

[24]  Johan Desmet,et al.  The dead-end elimination theorem and its use in protein side-chain positioning , 1992, Nature.

[25]  Robert E. Bruccoleri,et al.  Chain closure with bond angle variations , 1985 .

[26]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[27]  Binding by design , 1991, Nature.

[28]  M. Karplus,et al.  Prediction of the folding of short polypeptide segments by uniform conformational sampling , 1987, Biopolymers.

[29]  Andrew R. Leach,et al.  Automated conformational analysis: Directed conformational search using the A* algorithm , 1990 .