VCU Bioinformatics and Bioengineering Summer Institute

Reading: General molecular modeling
Reading: Description of HINT

Research Simulation Prediction of protein-RNA interaction
through molecular modeling Tuesday, June 17, 2003

Molecular Modeling I: Small Molecules

Topics

Forcefields: building and optimizing in 3-D
- Cyclohexane: boats and chairs
- Local and global minima
- More organic molecules, including a few recreational pharmaceuticals
Visualization tricks
- lines, sticks, balls and spacefill models
- surface rendering
Beating the local minima problem
- Systematic search
- Molecular dynamics

Background Material