Computational Biophysics Workshop - Champaign, Jul. 6-10, 2009
Program
Location:
-
Technology Room (just past elevators in hotel lobby)
Day 1: Introduction to Protein Structure and Dynamics - K.
Schulten
| 08:30-09:00 | Continental Breakfast |
| 09:00-09:10 | Opening Remarks |
| 09:10-10:40 | Structure and Sequence Analysis with VMD |
| Coffee Break | |
| 11:00-12:00 | VMD for Structure Building and Dynamics Analysis |
| 12:00-12:30 | Q & A |
| Lunch Break | |
| 14:00-15:30 | VMD Tutorial I |
| Coffee Break | |
| 16:00-18:00 | VMD Tutorial II |
Day 2: Statistical Mechanics of Proteins - K. Schulten
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Molecular Dynamics with NAMD I |
| Coffee Break | |
| 10:50-12:10 | Molecular Dynamics with NAMD II |
| 12:10-12:30 |
Q & A Group photo |
| Lunch Break | |
| 14:00-16:00 | NAMD Tutorial I |
| Coffee Break | |
| 16:15-18:00 | NAMD Tutorial II |
Day 3: Parameters for Classical Force Fields - E. Tajkhorshid
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Introduction to Topology, Parameters, and Structure Files |
| Coffee Break | |
| 10:50-12:10 | Examples and Applications |
| 12:10-12:30 | Q & A |
| Lunch Break | |
| 14:00-16:30 | Parameterizing a Novel Residue; Topology File Tutorial |
| Coffee Break | |
| 16:45-18:00 | Stretching Deca-alanine Tutorial |
Day 4: Simulating Membrane Channels - E. Tajkhorshid
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Introduction and Examples |
| Coffee Break | |
| 10:50-12:10 | Transport in Aquaporins; Nanotubes |
| 12:10-12:30 | Q & A |
| Lunch Break | |
| 14:00-16:30 | Membrane Proteins Tutorial |
| Coffee Break | |
| 16:45-18:00 | Simulation of Water Permeation Through Nanotubes/IMD |
Day 5: Introduction to Bioinformatics - Z. Luthey-Schulten
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD |
| Coffee Break | |
| 10:50-12:10 | Application of MultiSeq to Evolution of Translation Machinery |
| 12:10-12:30 | Q & A |
| Lunch Break | |
| 14:00-16:00 | Evolution of Translation Tutorials I & II: Class I Aminoacyl-tRNA Synthetases and the Elongation Factor Tu (EF-Tu:tRNA) |
| Coffee Break | |
| 16:15-18:00 | Evolution of Translation Tutorial III: tRNA and the Ribosome, or Bioinformatics Study of Aquaporins |
Note: program subject to change.
