Computer-Aided Molecular Design
Theory and ApplicationsBy
- Jean-Pierre Doucet, Universite de Paris 7-Denis Diderot
- Jacques Weber, Universite de Geneve, Suisse
The computer-aided design of novel molecular systems has undoubtedly reached the stage of a mature discipline offering a broad range of tools available to virtually any chemist. However, there are few books coveringmost of these techniques in a single volume and using a language which may generally be understood by students or chemists with a limited knowledge of theoretical chemistry. The purpose of this book is precisely to review, in such a language, both methodological aspects and important applications of computer-aided molecular design (CAMD), with a special emphasis on drug design and protein modeling.Using numerous examples ranging from molecular models to shapes, surfaces, and volumes, Computer-Aided Molecular Design provides coverage of the role molecular graphics play in CAMD. The text also treats the very notion of the structure of molecular systems by presenting both the various experimental techniques giving access to it and the most common model builders based on force fields. Separate chapters are devoted to other important topics in CAMD, such as Monte Carlo and molecular dynamics simulations; most common quantum chemical methods; derivation and visualization of molecular properties; and molecular similarity. Finally, strategies used in protein modeling and drug design, such as receptor mapping and the pharmacophore approach, are presented and illustrated by several examples.The book is addressed to students and researchers who wish to enter this new exciting field of molecular sciences, but also practitioners in CAMD as a comprehensive source of refreshing information in their field.
This book will appeal to a wide readership of researchers and students in all areas of chemistry, biology, biochemistry, and pharmacology, as well as to industrial chemists in pharmaceuticals.
Hardbound, 487 pages
Published: March 1996
Imprint: Academic Press
This is a very useful refernce and text for beginning and advanced researchers in molecular modeling. It should be strongly considered by instructors as a potential student text for academic or industrial courses in molecular modeling.
--Glen E. Kellogg in JOURNAL OF MEDICINAL CHEMISTRY
- 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.