The Annual Reports
in Computational Chemistry

Volume 4 - Table of Contents



Section 1: Bioinformatics (Section Editor: Wei Wang)

1. Structural Perspectives on Protein Evolution
        Eric Franzosa and Yu Xia
  1. Introduction
  2. Determinants of Evolutionary Rate
  3. Theoretical Advances
  4. Empirical Results: Single Proteins
  5. Empirical Results: Higher Order Properties
  6. Summation
  7. Acknowledgements
  8. References
2. Predicting Selectivity and Druggability in Drug Discovery
        Alan C. Cheng
  1. Introduction
  2. Selectivity
  3. Druggability
  4. Conclusions
  5. References

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

3. Machine Learning for Protein Structure and Function Prediction
        Robert Ezra Langlois and Hui Lu
  1. Introduction
  2. Machine Learning Problem Formulations
  3. Applications in Protein Structure and Function Modeling
  4. Discussion and Future Outlook
  5. Acknowledgements
  6. References
4. Modeling Protein–Protein and Protein–Nucleic Acid Interactions:
        Structure, Thermodynamics, and Kinetics

        Huan-Xiang Zhou, Sanbo Qin and Harianto Tjong
  1. Introduction
  2. Building Structural Models
  3. Prediction of Binding Affinities
  4. Prediction of Binding Rates
  5. Dynamics within Native Complexes and During Complex Formation
  6. Summary Points
  7. Acknowledgements
  8. References
5. Analyzing Protein NMR pH-Titration Curves
        Jens Erik Nielsen
  1. Introduction
  2. Fitting Protein NMR Titration Curves
  3. Conclusion and Outlook
  4. Acknowledgements
  5. References
6. Implicit Solvent Simulations of Biomolecules in Cellular Environments
        Michael Feig, Seiichiro Tanizaki and Maryam Sayadi
  1. Introduction
  2. Theory
  3. Applications and Challenges
  4. Summary and Outlook
  5. Acknowledgements
  6. References

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

7. Implicit Solvent Models in Molecular Dynamics Simulations: A Brief Overview
        Alexey Onufriev
  1. Introduction
  2. Implicit Solvent Framework
  3. Conclusions and Outlook
  4. Acknowledgements
  5. References
8. Comparing MD Simulations and NMR Relaxation Parameters
        Vance Wong and David A. Case
  1. Introduction
  2. Internal Motions and Flexibility
  3. Overall Tumbling and Rotational Diffusion
  4. Conclusions
  5. Acknowledgements
  6. References
9. Applications and Advances of QM/MM Methods in Computational Enzymology
        Alessio Lodola, Christopher J. Woods and Adrian J. Mulholland
  1. Introduction
  2. Recent Applications of QM/MM Methods to Enzymes
  3. Enzyme Conformational Changes and Fluctuations: Efficient Sampling in QM/MM Simulations
  4. Conclusion
  5. Acknowledgements
  6. 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
  1. Introduction
  2. Polymerization Kinetics Modeled by the Chemical Stochastic Equation
  3. Polymerization Events Modeled by Langevin Dynamics
  4. Numerical Simulations of the Polymerization Models
  5. Discussion
  6. Conclusion
  7. Acknowledgements
  8. References

Section 5: Emerging Technologies (Section Editor: Wendy Cornell)

11. SAR Knowledge Bases in Drug Discovery
          Stefan Senger and Andrew R. Leach
  1. Introduction
  2. Overview of SAR Knowledge Bases
  3. Comparison and Integration of Databases
  4. Applications of SAR Knowledge Bases
  5. Future Prospects
  6. Acknowledgements
  7. References
12. PubChem: Integrated Platform of Small Molecules and Biological Activities
          Evan E. Bolton, Yanli Wang, Paul A. Thiessen and Stephen H. Bryant
  1. Introduction
  2. Description
  3. Data Relationships
  4. Interface
  5. Tools
  6. Programmatic Tools
  7. Deposition System
  8. Future Directions
  9. Acknowledgements
  10. References

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