Annual Reports in Computational Chemistry, Volume 7

1st Edition

Editors: Ralph Wheeler
Paperback ISBN: 9780444538352
eBook ISBN: 9780444543028
Imprint: Elsevier
Published Date: 21st October 2011
Page Count: 288
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Table of Contents


Section 1: Bioinformatics


Potential Landscape and Flux Framework of Nonequilibrium Biological Networks

1. Introduction

2. Biochemical Oscillation

3. Stem-Cell Differentiation and Development: Arrows of Time


Section 2: Simulation Methodologies

Predicting Structural and Functional Properties of Membrane Proteins from Protein Sequence

1. Topologies and 3D Structures of Integral Membrane Proteins

2. Predicting TM Helices from Sequence

3. Predicting Structural Features of Helical TM Proteins

4. Predicting the Exposure Status of TM Residues

5. Topology and Exposure Status Prediction of TMB

6. Functional Classification of GPCRs and Membrane Transporters

7. Outlook

A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations

1. Introduction

2. Energy-Based Approach to Coarse-Graining

3. Force-Matching Approach to Coarse-Graining

4. Mixed Resolution Dynamics

5. Prospective Utilization

6. Outlook and Summary

An Overview of String-Based Path Sampling Methods

1. Introduction

2. Elastic Band Derived Methods

3. Applications

4. Conclusions and Outlook

Constructing and Evaluating Predictive Models for Protein Biophysical Characteristics

1. Introduction

2. Characterizing the Error Distribution

3. Outliers

4. Accurate Model Parameters

5. Conclusion

Supplementary Data

Section 3: Biological Modeling

Extracting Experimental Measurables from Molecular Dynamics Simulations of Membranes

1. Introduction

2. Bilayer Structure

3. Bilayer Dynamics

4. Future Direction: Escaping the Timescale Limit


Annual Reports in Computational Chemistry provides timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists.

Key Features

  • Broad coverage of computational chemistry and up-to-date information
  • Each chapter reviews the most recent literature on a specific topic of interest to computational chemists


Researchers and students interested in computational chemistry


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© Elsevier 2011
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About the Editors

Ralph Wheeler Editor

Affiliations and Expertise

Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA, USA