Annual Reports in Computational Chemistry, Volume 4

Section 1: Bioinformatics (Section Editor: Wei Wang)

1. Structural Perspectives on Protein Evolution Eric Franzosa and Yu Xia

2. Introduction

3. Determinants of Evolutionary Rate
4. Theoretical Advances
5. Empirical Results: Single Proteins
6. Empirical Results: Higher Order Properties

7. Summation Acknowledgements References

8. Predicting Selectivity and Druggability in Drug Discovery Alan C. Cheng

9. Introduction

10. Selectivity
11. Druggability
12. Conclusion References

Section 2: Biological Modeling (Section Editor: Nathan Barker)

1. Machine Learning for Protein Structure and Function Prediction Robert Ezra Langlois and Hui Lu

2. Introduction

3. Machine Learning Problem Formulations
4. Applications in Protein Structure and Function Modeling

5. Discussion and Future Outlook Acknowledgements References

6. Modeling Protein-Protein and Protein-Nucleic Acid Interactions: Structure, Thermodynamics, and Kinetics Huan-Xiang Zhou, Sanbo Qin and Harianto Tjong

7. Introduction

8. Building Structural Models
9. Prediction of Binding Affinities
10. Prediction of Binding Rates
11. Dynamics within Native Complexes and During Complex Formation
12. Summary Points References

1. Analysing Protein NMR pH-titration Curves Jens Erik Nielsen

2. Introduction

3. Fitting Protein Titration Curves

4. Conclusion and Outlook References

5. Implicit Solvent Simulations of Biomolecules in Cellular Environments Michael Feig, Seiichiro Tanizaki and Maryam Sayadi

6. Introduction

7. Theory
8. Applications and Challenges
9. Summary and Outlook Acknowledgements References

Section 3: Simulation Methodologies (Section Editor: Carlos Simmerling)

1. Implicit Solvent Models in Molecular Dynamics Simulations: A Brief Overview Alexey Onufriev

2. Introduction

3. Implicit Solvent Framework

4. Conclusions and Outlook Acknowledgments References

5. Comparing MD Simulations and NMR Relaxation Parameters Vance Wong and David A. Case

6. Introduction

7. Internal Motions and Flexibility
8. Overall Tumbling and Rotational Diffusion
9. Conclusions Acknowledgements References

Annual Reports in Computational Chemistry is a new periodical providing 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. Each volume is organized into (thematic) sections with contributions written by experts. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. Annual Reports in Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry.

• Broad coverage of computational chemistry and up-to-date information
• Topics covered include bioinformatics, drug discovery, protein NMR, simulation methodologies, and applications in academic and industrial settings
• Each chapter reviews the most recent literature on a specific topic of interest to computational chemists

Researchers and students interested in computational chemistry