Full Description
Ideal for beginners, this book explains the basics of modeling in a competent yet easily understandable way. Following complete sections on the modeling of small molecules, protein modeling and chemogenomics, completely worked-out examples show the way to the reader's first modeling experiment.
This new, third edition features a new chapter on chemogenomics, reflecting the trend towards 'chemical biology', as well as the protein modeling example being completely rewritten for a better 'feel' of modeling complex biomolecules.
The authors are experienced university teachers who regularly hold courses on molecular modeling, making this a tried-and-tested text for teachers. It is equally valuable for experts, since it is the only book to evaluate the strengths and limitations of the molecular modeling techniques and software currently available.
Contents
Introduction
Small Molecules
- Generation of 3D-Coordinates
- Computational Tools for Geometry Optimization
- Conformational Analysis
- Determination of Molecular Interaction Potentials
- Pharmacophore Identification
- 3D QSAR Methods
A Case Study for Small Molecule Modeling: Dopamine D3 Receptor Antagonists
- Building a Pharmacophore Model
- 3D QSAR Analysis
Introduction to Comparative Protein Modeling
- Where and How to get Information on Proteins
- Terminology and Principles of Protein Structure
- Comparative Protein Modeling
- Optimization Procedures -
Model Refinement -
Molecular Dynamics
- Validation of Protein Models
- Properties of Proteins
Virtual Screening and Docking
- Preparation of the Partners
- Docking Algorithms
- Scoring Functions
- Postfiltering Virtual Screening Results
- Comparison of Different Docking and Scoring Methods
- Examples of successful Virtual Screening Studies
Scope and Limits of Molecular Docking
- Docking in the Polar Active Site that Contains Water
- Including Cofactor in Docking? (NEW)
- Impact of Tautomerism on Docking (NEW)
Chemogenomic Approaches to Rational Drug Design (NEW)
- Description of Ligand and Target Spaces
- Ligand-based Chemogenomic Approaches
- Targed-based Chemogenomic Approaches
- Target-Ligand Based Chemogenomic Approaches
A Case Study for Protein Modeling: the Nuclear Hormone Receptor CAR as an Example for Comparative Modeling and the Analysis of Protein-Ligand Complexes (NEW)
- The Biochemical and Pharmacological Description of the Problem
- Comparative Modeling of the Human Nuclear Hormone Receptor CAR
- Analysis of the Models that Emerged from MD Simulations
- Analysis of CAR Mutants
- Modeling of CAR-Ligand Complexes
- The CAR X-Ray Structure Comes into Play
- Virtual Screening for Novel CAR Activators
