Computational Chemistry Methods in Structural Biology

Computational Chemistry Methods in Structural Biology

1st Edition - September 13, 2011

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  • Editor: Christo Christov
  • eBook ISBN: 9780123864864
  • Hardcover ISBN: 9780123864857

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Description

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

Readership

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

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

    Acknowledgment

    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

    Acknowledgments

    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

    Acknowledgments

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

    Abbreviations

    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

    Acknowledgments

Product details

  • No. of pages: 360
  • Language: English
  • Copyright: © Academic Press 2011
  • Published: September 13, 2011
  • Imprint: Academic Press
  • eBook ISBN: 9780123864864
  • Hardcover ISBN: 9780123864857

About the Serial Volume Editor

Christo Christov

Dr. Christo Z. Christov teaches at Northumbria University, Ellison Building, Newcastle-upon-Tyne, UK

Affiliations and Expertise

Department of Chemistry, Michigan Technological University, Houghton, MI, USA

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