## Rational Drug DesignDonald G. Truhlar, W. Jeffrey Howe, Anthony J. Hopfinger, Jeff Blaney, Richard E. Dammkoehler Drug research and discovery are of critical importance in human health care. Computational approaches for drug lead discovery and optimization have proven successful in many recent research programs. These methods have grown in their effectiveness not only because of improved understanding of the basic science - the biological events and molecular interactions that define a target for therapeutic intervention - but also because of advances in algorithms, representations, and mathematical procedures for studying such processes. This volume surveys some of those advances. A broad landscape of high-profile topics in computer-assisted molecular design (CAMD) directed to drug design are included. Subject areas represented in the volume include receptor-based applications such as binding energy approximations, molecular docking, and de novo design; non-receptor-based applications such as molecular similarity; molecular dynamics simulations; solvation and partitioning of a solute between aqueous and nonpolar media; graph theory; non-linear multidimensional optimization, processing of information obtained from simulation studies, global optimization and search strategies, and performance enhancement through parallel computing. |

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### Contents

IMPORTANT CURRENT PROBLEMS IN DRUG DESIGN THAT MAY BE COMPUTATIONALLY TRACTABLE | 1 |

NEW PROBLEMS THAT SHOULD BE ADDRESSED IN THE NEXT TEN YEARS | 7 |

MATCHING OF CHEMICAL AND BIOLOGICAL STRUCTURES USING SUBGRAPH AND MAXIMAL COMMON SUBGRAPH ISOMORPHISM ... | 11 |

MOLECULAR SIMILARITY | 39 |

MODELING THE EFFECT OF SOLVATION ON STRUCTURE REACTIVITY AND PARTITIONING OF ORGANIC SOLUTES UTILITY IN DRU... | 51 |

CELLBASED METHODS FOR SAMPLING IN HIGHDIMENSIONAL SPACES | 73 |

A PRELIMINARY MULTIOBJECTIVE ANALYSIS OF THE CHEMOTHERAPEUTIC BENEFITS OF HAIRPINLINKED POLYAMIDES | 81 |

USING STRUCTURAL INFORMATION FOR THE CREATIVE DESIGN OF MOLECULES | 93 |

RESULTS OF THE DESIGN AND SYNTHESIS OF A NOVEL INHIBITOR | 103 |

DEDUCING OBJECTIVE SITE MODELS BY MIXED INTEGER PROGRAMMING | 115 |

MOLECULAR DYNAMICS INFORMATION EXTRACTION | 127 |

IONIC CHARGING FREE ENERGIES USING EWALD SUMMATION | 149 |

EVOLUTIONARY CONSTRUCTION OF NOVEL INTERPRETABLE NONLINEAR MODELS OF EXPERIMENTAL DATA | 163 |

APPLICATIONS OF DISTRIBUTED COMPUTING TO CONFORMATIONAL SEARCHES | 191 |

### Other editions - View all

Rational Drug Design Donald G. Truhlar,W. Jeffrey Howe,Anthony J. Hopfinger,Jeff Blaney,Richard E. Dammkoehler No preview available - 2012 |

### Common terms and phrases

A-tracts acid analysis angle application Artymiuk atoms base pairs Binder binding biological BoHACEK boundary conditions calculated charge Chem chemical structures compounds contains CRAMER curvature cutoff data set database denoted descriptors dielectric dihedral angles dipole distance drug design effects electrostatic potential equation Ewald sum Ewald summation example experimental free energy function Genetic Algorithm geometry GFA model graph graph theory grid GrowMol helicoidals hydrogen bond imidazole inhibitors interactions kcal/mol large number lattice ligand linear LogP matching Mathematics MCS algorithm methods minor groove mode molecular dynamics molecules NaNO3 nodes nondominated nonlinear optimization p-loop parameterization parameters partitioning PEPTOR pharmacophore Phys polyamide population possible potency predict problem procedure protein pyrrole QSPR query samples screening sialidase simulations solution solvation solvent SrNO3 statistical struc subgraph isomorphism subset substructure searching surface target sequence techniques Theory thermolysin torsions TRUHLAR values variable vector Willett

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Page 205 - MJS Dewar, EG Zoebisch, EF Healy and JJP Stewart, J. Am. Chem. Soc. 107, 3902 (1985).