The Annual Reports
in Computational Chemistry
Volume 4 - Table of Contents
Contributors
Preface
Section 1: Bioinformatics (Section Editor: Wei Wang)
- 1. Structural Perspectives on Protein Evolution
Eric Franzosa and Yu Xia- Introduction
- Determinants of Evolutionary Rate
- Theoretical Advances
- Empirical Results: Single Proteins
- Empirical Results: Higher Order Properties
- Summation
- Acknowledgements
- References
- 2. Predicting Selectivity and Druggability in Drug Discovery
Alan C. Cheng- Introduction
- Selectivity
- Druggability
- Conclusions
- References
Section 2: Biological Modeling (Section Editor: Nathan Barker)
- 3. Machine Learning for Protein Structure and Function Prediction
Robert Ezra Langlois and Hui Lu- Introduction
- Machine Learning Problem Formulations
- Applications in Protein Structure and Function Modeling
- Discussion and Future Outlook
- Acknowledgements
- References
- 4. Modeling Protein–Protein and Protein–Nucleic Acid Interactions:
Structure, Thermodynamics, and Kinetics
Huan-Xiang Zhou, Sanbo Qin and Harianto Tjong- Introduction
- Building Structural Models
- Prediction of Binding Affinities
- Prediction of Binding Rates
- Dynamics within Native Complexes and During Complex Formation
- Summary Points
- Acknowledgements
- References
- 5. Analyzing Protein NMR pH-Titration Curves
Jens Erik Nielsen- Introduction
- Fitting Protein NMR Titration Curves
- Conclusion and Outlook
- Acknowledgements
- References
- 6. Implicit Solvent Simulations of Biomolecules in Cellular Environments
Michael Feig, Seiichiro Tanizaki and Maryam Sayadi- Introduction
- Theory
- Applications and Challenges
- Summary and Outlook
- Acknowledgements
- References
Section 3: Simulation Methodologies (Section Editor: Carlos Simmerling)
- 7. Implicit Solvent Models in Molecular Dynamics Simulations: A Brief Overview
Alexey Onufriev- Introduction
- Implicit Solvent Framework
- Conclusions and Outlook
- Acknowledgements
- References
- 8. Comparing MD Simulations and NMR Relaxation Parameters
Vance Wong and David A. Case- Introduction
- Internal Motions and Flexibility
- Overall Tumbling and Rotational Diffusion
- Conclusions
- Acknowledgements
- References
- 9. Applications and Advances of QM/MM Methods in Computational Enzymology
Alessio Lodola, Christopher J. Woods and Adrian J. Mulholland- Introduction
- Recent Applications of QM/MM Methods to Enzymes
- Enzyme Conformational Changes and Fluctuations: Efficient Sampling in QM/MM Simulations
- Conclusion
- Acknowledgements
- References
Section 4: Physical Modeling (Section Editor: Jeffrey D. Madura)
- 10. Stochastic Models for Polymerization Reactions Under Nonequilibrium Conditions
Yanping Qin, Alexander V. Popov and Rigoberto Hernandez- Introduction
- Polymerization Kinetics Modeled by the Chemical Stochastic Equation
- Polymerization Events Modeled by Langevin Dynamics
- Numerical Simulations of the Polymerization Models
- Discussion
- Conclusion
- Acknowledgements
- References
Section 5: Emerging Technologies (Section Editor: Wendy Cornell)
- 11. SAR Knowledge Bases in Drug Discovery
Stefan Senger and Andrew R. Leach- Introduction
- Overview of SAR Knowledge Bases
- Comparison and Integration of Databases
- Applications of SAR Knowledge Bases
- Future Prospects
- Acknowledgements
- References
- 12. PubChem: Integrated Platform of Small Molecules and Biological Activities
Evan E. Bolton, Yanli Wang, Paul A. Thiessen and Stephen H. Bryant- Introduction
- Description
- Data Relationships
- Interface
- Tools
- Programmatic Tools
- Deposition System
- Future Directions
- Acknowledgements
- References
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