Molecular modeling : basic principles and applications / / Hans-Dieter Höltje and Gerd Folkers

• Record Nr.: UNINA9910829906903321
• Autore: Höltje Hans-Dieter
• Pubbl/distr/stampa: Weinheim, Germany ; ; New York, New York : , : John Wiley & Sons, , [1997]; ©1997
• ISBN: 1-281-75846-9; 9786611758462; 3-527-61477-X; 3-527-61476-1
• Descrizione fisica: 1 online resource (209 p.)
• Collana: Methods and principles in medicinal chemistry ; ; v. 5
• Disciplina: 572/.33/0113
• Soggetti: Molecules - Models - Computer simulation; Ligand binding (Biochemistry) - Computer simulation; Biomolecules - Structure - Computer simulation; Drugs - Design - Computer simulation
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Note generali: Description based upon print version of record.
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: Molecular Modeling; Preface; A Personal Foreword; Contents; 1 Introduction; 1.1 Modern History of Molecular Modeling; 1.2 Do Today's Molecular Modeling Methods Illustrate only the Lukretian World?; 1.3 What are Models Used for?; 1.4 Molecular Modeling Uses All FourTypes for Model Building; 1.5 The Final Step is Design; 1.6 The Scope of the Book; 2 Small Molecules; 2.1 Generation of 3D Coordinates; 2.1.1 Crystal Data; 2.1.2 Fragment Libraries; 2.1.3 Sketch Approach; 2.2 Computational Tools for Geometry Optimization; 2.2.1 Force Fields; 2.2.2 Geometry Optimization; 2.2.3 Energy-Minimizing Procedures2.2.3.1 Steepest Descent Minimizer; 2.2.3.2 Conjugate Gradient Method; 2.2.3.3 Newton-Raphson Minimizer; 2.2.4 Use of Charges, Solvation Effects; 2.2.5 Quantum Mechanical Methods; 2.2.5.1 Ab initio Methods; 2.2.5.2 Semiempirical Molecular Orbital Methods; 2.3 Conformational Analysis; 2.3.1 Conformational Analysis Using Systematic Search Procedures; ; 2.3.2 Conformational Analysis Using Monte Carlo Methods; 2.3.3 Conformational Analysis Using Molecular Dynamics; 2.4 Determination of Molecular Interaction Potentials; 2.4.1 Molecular Electrostatic Potentials (MEPs)2.4.1.1 Methods for Calculating Atomic Point Charges; 2.4.1.2 Methods for Generating MEPs; 2.4.2 Molecular Interaction Fields; 2.4.2.1 Calculation of GRID Fields; 2.4.2.2 How GRID Fields can be Exploited; 2.4.2.3 Use of Chemometrics:The CoMFA Method; 2.4.3 Hydrophobic Interactions; 2.4.3.1 Log P as a Measure of Lipophilicity; 2.4.3.2 The Hydropathic Field; 2.4.3.3 Display of Properties on a Molecular Surface; 2.5 Pharmacophore Identification; 2.5.1 Molecules to be Matched; 2.5.2 Atom-by-Atom Superposition; 2.5.3 Superposition of Molecular Fields; 2.6 The Use of Data Bants2.6.1 Conversion of 2D Structural Data into 3D Form; 2.6.2 3D Searching; 3 Example for Small Molecule Modeling: Serotonin Receptor Ligands; 3.1 Definition of the Serotoninergic Pharmacophore; 3.2 The Molecular Interaction Field; 3.3 Construction of a 5-HT 2a Receptor Binding Site Model; 3.4 Calculation of Interaction Energies; 3.5 Validation of the Model; 4 Introduction to Protein Modeling; 4.1 Where and How to get Information on Proteins; 4.2 Terminology and Principles of Protein Structure; 4.2.1 Conformational Properties of Proteins; 4.2.2 Types of Secondary Structural Elements4.2.2.1 The α-Helix; 4.2.2.2 The β-Sheet; 4.2.2.3 Turns; 4.2.3 Homologous Proteins; 4.3 Knowledge-Based Protein Modeling; 4.3.1 Procedures for Sequence Alignments; 4.3.2 Determination and Generation of Structurally Conserved Regions (SCRs); 4.3.3 Construction of Structurally Variable Regions (SVRs); 4.3.4 Side Chain Modeling; 4.3.5 Distance Geometry Approach; 4.3.6 Secondary Structure Prediction; 4.3.7 Energy-Based Modeling Methods; 4.4 Optimization Procedures - Model Refinement - Molecular Dynamics; 4.4.1 Force Fields for Protein Modeling; 4.4.2 Geometry Optimization
• Sommario/riassunto: Written by experienced experts in molecular modeling, this books describes the basics to the extent that is necessary if one wants to be able to reliably judge the results from molecular modeling calculations. Its main objective is the description of the various pitfalls to be avoided. Without unnecessary overhead it leads the reader from simple calculations on small molecules to the modeling of proteins and other relevant biomolecules.A textbook for beginners as well as an invaluable reference for all those dealing with molecular modeling in their daily work!