Computational Biophysics Workshop
Program
Day 1: Introduction to Protein Structure and Dynamics
| 09:00-09:10 | Opening Remarks |
| 09:10-10:40 | Structure and Sequence Analysis with VMD |
| Coffee Break | |
| 11:00-12:10 | VMD for Structure Building and Dynamics Analysis |
| 12:10-12:30 | 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
| 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: Introduction to Bioinformatics
| 09:00-10:30 | Introduction to Bioinformatics: Sequence,
Structure, and Alignment Evolutionary Concepts in Bioinformatics |
| Coffee Break | |
| 10:50-12:10 | Application of Bioinformatics |
| 12:10-12:30 | Q & A |
| Lunch Break | |
| 14:00-16:00 | Evolution of Protein Structure - Aspartyl tRNA Synthetase |
| Coffee Break | |
| 16:15-18:00 | Sequence Alignment Algorithms/Bioinformatics Study of Aquaporins |
Day 4: Parameters for Classical Force Fields
| 09:00-10:30 | Molecular Dynamics of Cellular Processes I |
| Coffee Break | |
| 10:50-12:10 | Molecular Dynamics of Cellular Processes II |
| 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 | Nanotube Tutorial / Stretching Deca-alanine Tutorial |
Day 5: Simulating Membrane Channels
| 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 | Nanotubes/IMD |
| Coffee Break | |
| 16:45-18:00 | Stretching Deca-alanine/Open tutorial work time |
Note: program subject to change.
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