Computational Chemistry Methods in Structural Biology - 1st Edition - ISBN: 9780123864857, 9780123864864

Computational Chemistry Methods in Structural Biology, Volume 85

1st Edition

Serial Volume Editors: Christo Christov
eBook ISBN: 9780123864864
Hardcover ISBN: 9780123864857
Imprint: Academic Press
Published Date: 23rd September 2011
Page Count: 360
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Table of Contents

Application of Computational Methods to the Design of Fatty Acid Amide Hydrolase (FAAH) Inhibitors Based on a Carbamic Template Structure

I. Introduction

II. Ligand-Based Drug Design

III. Structure-Based Drug Design

IV. Recent Advances

Recent theoretical and computational advances for modeling protein–ligand binding affinities

I. Introduction

II. Theory of Noncovalent Binding

III. Computational Methods

IV. Conclusions


Hybrid Schemes Based on Quantum Mechanics/Molecular Mechanics Simulations

I. Introduction: State of Art

II. Potential of Mean Force/Free-Energy Calculations

III. Applications

IV. Conclusions and Outlook


Exploring Membrane and Protein Dynamics with Dissipative Particle Dynamics

I. Introduction

II. Setting Up DPD Simulations

III. Investigating Structure and Dynamics of Membranes with DPD

Coarse-grained Representation of Protein Flexibility. Foundations, Successes, and Shortcomings

I. Introduction

II. Coarse-Grained Potentials

III. Sampling Techniques

IV. Conclusions

Recent Advances in the Molecular Modeling of Estrogen Receptor-Mediated Toxicity

I. Introduction

II. Structural Studies of the Estrogen Receptor and Its Ligands

III. Molecular Modeling Approaches to Investigate Estrogen Receptor-Mediated Toxicological Effects

IV. Molecular Modeling of Estrogen Receptor-Mediated Toxicological Effects: Case Studies

V. Conclusions


Multiscale computational methods for mapping conformational ensembles of G-protein-coupled receptors


I. Introduction

II. Conformational Flexibility in GPCRs

III. Computational Approaches for Studying Conformational Ensembles of GPCRs

IV. Activation Mechanism of GPCRs

V. Concluding Remarks

Advances in Implicit Models of Water Solvent to Compute Conformational Free Energy and Molecular Dynamics of Proteins at Constant pH

I. Introduction

II. Formulation of General Implicit Solvent Model for Calculating Conformational Free Energy

III. Continuum Solvent Models

IV. Protein Ionization

V. Examples of Simulations with Implicit Solvent Models



Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This volume features articles on Computational Chemistry methods in Structural Biology.

Key Features

  • Essential resource for protein chemists
  • This volume features articles on Computational Chemistry methods in Structural Biology


Biochemists, biophysicists, cell biologists, protein chemists, structural geneticists, and structural biologists


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© Academic Press 2011
Academic Press
eBook ISBN:
Hardcover ISBN:

About the Serial Volume Editors

Christo Christov Serial Volume Editor

Affiliations and Expertise

Northumbria University, UK