Computational Molecular Biophysics Lab Exercises

Fall, 2006

Professors Fetrow and Salsbury

• Lab Exercise 1: Physical models of proteins
• Lab Exercise 2: Introduction to macromolecular visualization and VMD
• Lab Exercise 3: PDB file formats and macromolecular visualization, part 2
• Lab Exercise 4: Introduction to MatLab and exploration of molecular forces
• Lab Exercise 5: Helix-coil transitions
• Lab Exercise 6 : Introduction to MD simulations and DEAC cluster use (intro to research paper)
• Lab Exercise 7 : Introduction to MD simulations in explicit solvent
• Lab Exercise 8 : Analysis of MD simulations