Computer-Aided Molecular Design (eBook)

Theory and Applications

Jean-Pierre Doucet, Jacques Weber (Autoren)

eBook Download: PDF

1996 | 1. Auflage
487 Seiten
Elsevier Science (Verlag)
978-0-08-052974-5 (ISBN)

Infos

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.

Key Features
* Presents a comprehensive introduction to computer-aided molecular design
* Describes applications of CAMD through the use of numerous examples
* Emphasizes strategies used in protein modeling and drug design
* Includes separate chapters devoted to other important topics in CAMD, such as:
* Monte Carlo and molecular dynamics simulations
* Common quantum chemical methods
* Derivation and visualization of molecular properties
* Molecular similarity

Inhalt

Cover 1
Contents 6
Preface 8
Acknowledgements 10
Introduction 18
Chapter 1. Computer graphics: an introduction 22
1.1 Display and input devices 23
1.2 Elementary graphics primitives 30
1.3 Geometrical transformations 38
Chapter 2. Computer graphics: towards realistic images 44
2.1 Representation of 3D objects 45
2.2 Viewing, windowing and clipping 52
2.3 Segments 58
2.4 Hidden lines and surfaces removal 59
2.5 Rendering 70
Chapter 3. Displaying molecular shapes 80
3.1 Representation of structural shapes 82
3.2 Representation of property shapes 91
3.3 Concluding remarks: symbolic pictorial primitives 99
Chapter 4. Access to experimental geometrical parameters 102
4.1 Crystals and X-ray diffraction 103
4.2 Neutron scattering and miscellaneous techniques 110
4.3 NMR: a source of geometrical data in solution 113
4.4 The Cambridge Structural Database 124
4.5 The Brookhaven Protein Data Bank 139
4.6 Databases of calculated structures 141
Chapter 5. Empirical force field methods and molecular mechanics 145
5.1 The force field 148
5.2 Steric energy and derived information: strain energy and heat of formation 160
5.3 Search for the preferred geometry and energy minimization 161
5.4 Molecular mechanics: scope, limitations and evolution 165
5.5 Some applications 172
5.6 Trends and prospects 186
Chapter 6. Monte Carlo and molecular dynamics simulations 192
6.1 Monte Carlo simulations 193
6.2 Molecular dynamics simulations 204
Chapter 7. Exploring the conformational space: distance geometry and model builders 218
7.1 Distance geometry 221
7.2 Exploring the conformational space 227
7.3 Model builders 241
Chapter 8. Molecular surfaces and volumes 260
8.1 Definition of molecular volumes 261
8.2 Analytical evaluations of surfaces or volumes 264
8.3 Numerical methods 268
8.4 Boolean operations and molecular comparisons 277
8.5 Towards quantitative relationships 278
8.6 Concluding remarks: roughness and fractal surfaces 282
Chapter 9. Key features of quantum chemistry methods used in CAMD 287
9.1 The time-independent Schrödinger equation 290
9.2 Hartree-Fock and Roothaan equations: AB initio methods 294
9.3 Semi-empirical methods 303
9.4 Density functional methods 314
Chapter 10. Derivation and visualization of molecular properties 322
10.1 Molecular orbitals 322
10.2 Electron densities 329
10.3 Electrostatic properties 332
10.4 Reactivity indices 340
Chapter 11. Molecular similarity 349
11.1 Geometrical comparisons: molecular superimposition 353
11.2 Common substructure searches 361
11.3 Similarity between structural shapes 373
Chapter 12. Drug receptor interactions: receptor mapping and pharmacophore approach 384
12.1 The pharmacophore hypothesis 385
12.2 Active conformations of a drug: feasible binding modes of a ligand molecule at the receptor site 388
Chapter 13. Modelling proteins 426
13.1 Structural analysis 429
13.2 Representation 432
13.3 Determination of geometrical data: 2D NMR in protein structural analysis 436
13.4 Computer building 447
13.5 Knowledge-based prediction: model building from homology 452
13.6 Evaluating similarity 468
Subject index 484
Author index 496
Colour plate section 510

Produkt-Details

• Erscheint lt. Verlag: 5.3.1996
• Sprache: englisch
• Themenwelt: Sachbuch/Ratgeber
• Themenwelt: Informatik ► Weitere Themen ► CAD-Programme
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Chemie ► Analytische Chemie
• Themenwelt: Naturwissenschaften ► Chemie ► Physikalische Chemie
• Themenwelt: Naturwissenschaften ► Geowissenschaften ► Mineralogie / Paläontologie
• Themenwelt: Technik
• ISBN-10: 0-08-052974-7 / 0080529747
• ISBN-13: 978-0-08-052974-5 / 9780080529745