1993

Dynamic and Stochastic Protein Simulations:
From Peptides to Viruses

Alan Martin Mathiowetz

October 30, 1992

©1993
Alan Martin Mathiowetz
All Rights Reserved

To Laura.

• Acknowledgements
• Thesis Abstract
• Contents
• List of Figures
• List of Tables
• Chapter 1
  • Protein Simulations
  • Molecular Mechanics
    • Forcefields
    • Energy Minimization
    • Molecular Dynamics
  • Monte Carlo
• References
• Chapter 2
  • Introduction
  • Methodology
  • Results
    • Timing
    • Energy Fluctuations
    • Dihedral Distributions
  • Conclusions
• Leapfrog Verlet for Internal Coordinates
• Chapter 3
• Introduction
• Methodology
• Results
• Conclusions
• Chapter 4
• Introduction
• Methodology
  • The Protein Database Subset
  • Backbone () Probability Grids
  • Sidechain () Probability Grids
  • Note on Computations
• Conformations of Met-Enkephalin
• Conclusions
• Chapter 5
• Introduction
• Methodology
  • General Methodology
  • Variables
• Results
  • Crambin
  • Larger Proteins
• The C Forcefield
• Conclusions
• Chapter 6
• Introduction
• Methodology
• Antibody Hypervariable Loops
• Conclusions
• About this document ...