Computer-Aided Molecular Design: Theory and Applications

Computer Graphics: an Introduction: Display and Input Devices. Elementary Graphics Primitives. Geometrical Transformations. Computer Graphics: towards Realistic Images: Representation of 3D Objects. Viewing, Windowing and Clipping. Segments. Hidden Lines and Surfaces Removal. Rendering. Displaying Molecular Shapes: Representation of Structural Shapes. Representation of Property Shapes. Concluding Remarks: Symbolic Pictorial Primitives. Access to Experimental Geometrical Parameters: Crystals and X-ray Diffraction. Neutron Scattering and Miscellaneous Techniques. NMR: a Source of Geometrical Data in Solution. The Cambridge Structural Database. The Brookhaven Protein Data Bank. Databases of Calculated Structures. Empirical Force Field Methods and Molecular Mechanics: The Force Field. Steric Energy and Derived Information: Strain Energy and Heat of Formation. Search for the Preferred Geometry and Energy Minimization. Molecular Mechanics: Scope, Limitations and Evolution. Some Applications. Trends and Prospects. Monte Carlo and Molecular Dynamics Simulations: Monte Carlo Simulations. Molecular Dynamics Simulations. Exploring the Conformational Space: Distance Geometry and Model Builders: Distance Geometry. Exploring the Conformational Space. Model Builders. Molecular Surfaces and Volumes: Definition of Molecular Volumes. Analytical Evaluations of Surfaces or Volumes. Numerical Methods. Boolean Operations and Molecular Comparisons. Towards Quantitative Relationships. Concluding Remarks: Roughness and Fractal Surfaces. Key Features of Quantum Chemistry Methods used in CAMD: The Time-Independent Schridinger Equation. Hartree-Fock and Roothaan Equations: AB initio Methods. Semi-Empirical Methods. Density Functional Methods. Derivation and Visualization of Molecular Properties: Molecular Orbitals. Electron Densities. Electrostatic Properties. Reactivity Indices. Molecular Similarity: Geometrical Comparisons: Molecular Superimposition. Common Substructure Searches. Similarity between Structural Shapes. Drug Receptor Interactions: Reception Mapping and Pharmacophore Approach: The Pharmacophore Hypothesis. Active Conformations of a Drug: Feasible Binding Modes of a Ligand Molecule at the Receptor Site. Modelling Proteins: Structural Analysis. Representation. Determination of Geometrical Data: 2D NMR in Protein Structural Analysis. Computer Building. Knowledge-Based Prediction: Model Building From Homology.Evaluating Similarity. Subject Index. Author Index. Colour Plate Section.