Molecular Modeling. 3rd Edition

  • ID: 2183115
  • Book
  • 320 Pages
  • John Wiley and Sons Ltd
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Creating a computer model of a molecule with known or unknown structure that can then be studied by computational means is a key skill for biochemists, molecular biologists and aspiring drug developers. Increasingly sophisticated modeling software requires at least a basic understanding of the method in order to avoid misinterpretation of the data generated.

Ideal for beginners, this book explains the basics of modeling in a competent yet easily understandable way, with completely worked–out examples to guide readers to their first modeling experiments.

This third edition features a new chapter on chemogenomics, reflecting the trend towards ′chemical biology′, while the example of protein modeling is completely rewritten for a better ′feel′ of modeling complex biomolecules.

The authors are experienced university lecturers 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.
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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

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"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)

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