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 | ||
Bibliography | ||
References |