| Week (text chapter) | Lab Exercises |
| 1 Origins of structural information, goals of modeling and simulations, properties addressable by computation, data bases, types of renderings | Exercise 1. Elementary Unix, file manipulations,
databases, WWW resources, using SYBYL
Report due: January 18 |
| 2 Potential energy surfaces, QM and empirical force fields, parameterization, treatments of electrostatics, commercial software packages, energy units, charge classes | Exercise 2. Representation of structural
motifs in biological macromolecules, molecular surfaces; production of
printable representations; use of spreadsheets
Report due: January 25 |
| 3 Minimization, conformational searching, comparison of structures | Exercise 3. Building from scratch, conformational
energy minimization; energy minimization contest
Report due: February 8
|
| Project pre-proposal is due by February 11. | |
| 4 Dealing with solvent | Exercise 4. Molecular dynamics
Report due: February 20 |
| 5 Dynamics, methods, assumptions, time scales, utility; analysis methods, boundary effects, simulated annealing | Exercise 5. Homology modeling
Exercise 6. Docking to a receptor Report due: March 15 |
| 6 Connections to thermodynamics, Monte Carlo methods | Project completion;oral reports to be completed during the week of March 11. |
| 7 Receptor structure prediction, homology modeling, threading | |
| 8 Docking, lead discovery and optimization | |
| 9 Ligand design and docking, electrostatics and binding; review and catch up | Project completion;written report to be completed by March 15. |
| 10 Student oral reports | Final Exam: Friday, March 22, 8-11 am. |