Molecular Modeling and Simulation: An Interdisciplinary Guide

Tamar Schlick

List of Tables

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  (PDF)
Appendix B Article Reading List
Appendix C General Reference List
Appendix D Homeworks

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