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.
"Beginners as well as experts in the field of biochemistry, molecular biology, and drug development will find this book quite handy and useful. The third edition is justified given the rapid development of hardware and software tools and other advances in the applications of molecular modeling techniques." ( Doody' s, April 2009) "The authors are experienced university lecturers and as a result of their teaching practices the textbook provides teachers with a tried-and-tested learning material. The text is equally valuable to experts" (International Journal of Bioautomation , April 2009) "An excellent resource as an introduction to molecular modelling techniques ... .I can particularly recommend this book to academics." ( Journal of Medicinal Chemistry , September 2008)
Didier Rognan leads the Drug Bioinformatics Group at the Laboratory for Molecular Pharmacochemistry in Illkirch (France). He obtained a graduate degree in Pharmacy from the University of Rennes and completed his PhD in Medicinal Chemistry at the University of Strasbourg under the supervision of Camille G. Wermuth in 1989. Moving to the Swiss Federal Institute of Technology in Zürich he became Assistant Professor at the ETH before being named a research director at the CRNS in Illkirch near Strasbourg in 2000. Professor Rognan is mainly interested in all aspects (method development, applications) of protein-based drug design and virtual screening.
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