Molecular Modeling Basic Principles and Applications

ISBN-10: 3527315683

ISBN-13: 9783527315680

Edition: 3rd 2008

List price: $95.00
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Description:

Written by experienced experts in molecular modeling, this text describes the basics to the extent that is necessary to reliably judge the results from molecular modeling calculations.
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Book details

List price: $95.00
Edition: 3rd
Copyright year: 2008
Publisher: John Wiley & Sons, Incorporated
Publication date: 2/26/2008
Binding: Paperback
Pages: 320
Size: 6.50" wide x 9.50" long x 0.75" tall
Weight: 1.342
Language: English

The editors are based at the Amsterdam Center for Drug Research, a cross-disciplinary center in the Dutch academic system, but with numerous ties to pharmaceutical companies.

Hans-Dieter H_ltje is director of the Institute of Pharmaceutical Chemistry at the Heinrich-Heine-Universit+t D8sseldorf (Germany) where he also holds the chair of Medicinal Chemistry. His main interest is the molecular mechanism of drug action.Wolfgang Sippl is Professor of Pharmaceutical Chemistry at the Martin-Luther-University of Halle-Wittenberg (Germany). He is interested in 3D QSAR, molecular docking and molecular dynamics, and their applications in drug design and pharmacokinetics.Didier Rognan leads the Drug Bioinformatics Group at the Laboratory for Molecular Pharmacochemistry in Illkirch (France). He is mainly interested in all aspects (method development, applications) of protein-based drug design and virtual screening.Gerd Folkers is Professor of Pharmaceutical Chemistry at the ETH Z8rich (Switzerland). The focus of his research is the molecular interation between drugs and their binding sites.

Preface to the Third Edition
Introduction
Modern History of Molecular Modeling
Do Today's Molecular Modeling Methods Only Make Pictures of the Lukretian World or Do They Make Anything More?
What are Models Used For?
Molecular Modeling Uses all Four Kinds for Model Building
The Final Step Is Design
Scope of the Book
Small Molecules
Generation of 3D Coordinates
Crystal Data
Fragment Libraries
Conversion of 2D Structural Data into 3D Form
References
Computational Tools for Geometry Optimization
Force Fields
Geometry Optimization
Energy-minimizing Procedures
Use of Charges, Solvation Effects
Quantum Mechanical Methods
References
Conformational Analysis
Conformational Analysis Using Systematic Search Procedures
Conformational Analysis Using Monte Carlo Methods
Conformational Analysis Using Molecular Dynamics
Which Is the Method of Choice?
References
Determination of Molecular Interaction Potentials
Molecular Electrostatic Potentials (MEPs)
Molecular Interaction Fields
Display of Properties on a Molecular Surface
References
Further Reading
Pharmacophore Identification
Molecules to be Matched
Atom-by-atom Superposition
Superposition of Molecular Fields
References
3D QSAR Methods
The CoMFA Method
Other CoMFA-related Methods
More 3D QSAR Methods
Receptor-based 3D QSAR
Reliability of 3D QSAR Models
References
Further Reading
A Case Study for Small Molecule Modeling: Dopamine D[subscript 3] Receptor Antagonists
A Pharmacophore Model for Dopamine D[subscript 3] Receptor Antagonists
The Aromatic-Basic Fragment
The Spacer
The Aromatic-Amidic Residue
Resulting Pharmacophore
Molecular Interaction Fields
3D QSAR Analysis
Variable Reduction and PLS Model
Validation of the Model
Prediction of External Ligands
References
Introduction to Comparative Protein Modeling
Where and How to Get Information on Proteins
References
Terminology and Principles of Protein Structure
Conformational Properties of Proteins
Types of Secondary Structural Elements
Homologous Proteins
References
Comparative Protein Modeling
Procedures for Sequence Alignments
Determination and Generation of Structurally Conserved Regions (SCRs)
Construction of Structurally Variable Regions (SVRs)
Side-Chain Modeling
Distance Geometry Approach
Secondary Structure Prediction
Threading Methods
References
Optimization Procedures - Model Refinement - Molecular Dynamics
Force Fields for Protein Modeling
Geometry Optimization
The Use of Molecular Dynamics Simulations in Model Refinement
Treatment of Solvated Systems
Ligand-binding Site Complexes
References
Validation of Protein Models
Stereochemical Accuracy
Packing Quality
Folding Reliability
References
Properties of Proteins
Electrostatic Potential
Interaction Potentials
Hydrophobicity
References
Virtual Screening and Docking
Preparation of the Partners
Preparation of the Compound Library
Representation of Proteins and Ligands
Docking Algorithms
Incremental Construction Methods
Genetic Algorithms
Tabu Search
Simulated Annealing and Monte Carlo Simulations
Shape-fitting Methods
Miscellaneous Approaches
Scoring Functions
Empirical Scoring Functions
Force-field-based Scoring Functions
Knowledge-based Scoring Functions
Critical Overview of Fast Scoring Functions
Postfiltering Virtual Screening Results
Filtering by Topological Properties
Filtering by Consensus Mining Approaches
Filtering by Combining Computational Procedures
Filtering by Chemical Diversity
Filtering by Visual Inspection
Comparison of Different Docking and Scoring Methods
Examples of Successful Virtual Screening Studies
Outlook
References
Scope and Limits of Molecular Docking
Docking in the Polar Active Site that Contains Water Molecules
Including Cofactor in Docking?
Impact of Tautomerism on Docking
References
Further Reading
Chemogenomic Approaches to Rational Drug Design
Description of Ligand and Target Spaces
Ligand Space
Target Space
Protein-Ligand Space
Ligand-based Chemogenomic Approaches
Annotating Ligand Libraries
Privileged Structures
Ligand-based In silico Screening
Target-based Chemogenomic Approaches
Sequence-based Comparisons
Structure-based Comparisons
Target-Ligand-based Chemogenomic Approaches
Chemical Annotation of Target Binding Sites
Two-dimensional Searches
Three-dimensional Searches
Concluding Remarks
References
A Case Study for Protein Modeling: the Nuclear Hormone Receptor CAR as an Example for Comparative Modeling and the Analysis of Protein-Ligand Complexes
The Biochemical and Pharmacological Description of the Problem
Nuclear Hormone Receptor Superfamily
Molecular Architecture and Activation Mechanisms of Nuclear Hormone Receptors
The Human Constitutive Active Androstan Receptor (CAR)
CAR Ligands
Comparative Modeling of the Human Nuclear Hormone Receptor CAR
Choosing Appropriate Template Structures
Homology Modeling of the Human CAR
Setting up the System for the Molecular Dynamics Simulations
Analysis of the Models that Emerged from MD Simulations
Atomic Fluctuations
AF-2 Interaction Domain
Deciphering the Structural Basis for Constitutive Activity of Human CAR
Coactivator Binding
Analysis of CAR Mutants
Identifying Important Amino Acids for CAR Activation
MD Simulations of Selected CAR Mutants
Modeling of CAR-Ligand Complexes
The CAR X-ray Structure Comes into Play
How Accurate is the Generated CAR Model?
Docking Studies Using the CAR X-ray Structure
The Basis for Constitutive Activity Revisited
Virtual Screening for Novel CAR Activators
Concluding Remarks
References
Index
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