Molecular Modeling and Simulation: Contents

Molecular Modeling and Simulation: An Interdisciplinary Guide

1	Biomolecular Sructure and Modeling: Historical Perspective
	1.1 Structural biology chronology 1.2 Biomolecular simulation evolution
2	Biomolecular Structure and Modeling: Problem and Application Perspective
	2.1 Protein databases
3	Protein Basic
	3.1 Amino acid frequency
4	Protein Hierarchy

5	Nucleic Acids Structure
	5.1 Genetic code 5.2 Nucleic acid dihedral angle definitions 5.3 Mean properties of representative DNA forms 5.4 Selected parameters for model DNA helices
6	Topics in Nucleic Acids Structure
	6.1 Base-pair step parameters for free and protein-bound DNA 6.2 Protein/DNA complexes 6.3 DNA content of representative genomes
7	Theoretical Approaches
	7.1 Some CHARMM atom types
8	Force Fields
	8.1 Characteristic stretching vibrational frequencies 8.2 Characteristic bending and torsional vibrational frequencies 8.3 Examples of torsional potentials
9	Nonbonded Computations
	9.1 CPU time for nonbonded calculations
10	Multivariate Minimization
	10.1 Optimization software 10.2 Minimization comparisons
11	Monte Carlo Techniques
	11.1 MC calculations for
12	Molecular Dynamics: Basics
	12.1 Biomolecular sampling methods 12.2 High-frequency modes 12.3 Biomolecular timescales
13	Molecular Dynamics: Further Topics
	13.1 Verlet timestep restriction timescales 13.2 Stability limits
14	Similarity and Diversity

Appendix A Syllabus (Postscript) (PDF)
Appendix B Article Reading List
Appendix C General Reference List
Appendix D Homeworks
Bibliography
References