Agenda: Hands-on Workshop on Computational Biophysics 2013
Agenda: Hands-on Workshop on Computational Biophysics
Workshop details: Homepage Instructors Evaluations
Mon, June 10: Introduction to Protein Structure and Dynamics - Klaus Schulten
| 08:00-08:30 | Registration and Continental Breakfast |
| 08:30-09:00 | Welcome and Brief Overview - Ivet Bahar (video) |
| 09:00-09:10 | Opening Remarks (video) |
| 09:10-10:30 | Structure and Sequence Analysis with VMD (video) |
| Coffee Break | |
| 10:50-12:00 | Introduction to Molecular Dynamics with NAMD (video) |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 1400-16:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
| Coffee Break | |
| `6:15-18:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Tue, June 11: Statistical Mechanics of Proteins; Force Field Parameterization- Klaus Schulten and Emad Tajkhorshid
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Applications of VMD / NAMD in Modern Research (video1, video2) |
| Coffee Break | |
| 10:50- noon | Topology, Parameters, and Structure Files (video) |
| 12:00-12:30 pm | Q & A; Group picture |
| Lunch Break | |
| 14:00-16:00 pm |
Participant tutorial options: |
| Coffee Break | |
| 16:15-18:00 pm | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine, or 2) Expert NAMD Set Tutorials* 3) Parameterizing a Novel Residue 4) Topology File Tutorial |
| Dinner Break | (note: participants are on their own for this meal) |
| 19:00-21:00 | Presentations by workshop participants |
Wed, June 12: Simulating Membrane Proteins - Emad Tajkhorshid
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Introduction and Examples |
| Coffee Break | |
| 10:50-12:00 | Transport in Membrane Channels (video) |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-16:30 | Participant tutorial options: 1) Membrane Proteins 2) Open tutorial time |
| Coffee Break | |
| 16:45-18:00 | Participant tutorial options: 1) Membrane Proteins 2) Open tutorial time |
Thu, June 13: Collective Dynamics of Proteins Using Elastic Network Models - Ivet Bahar, Tim Lezon and Ahmet Bakan
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Elastic Network Models (ENMs) and Collective Motions of Biomolecular Systems using ProDy (video1, video2) |
| Coffee Break | |
| 10:50-12:00 | ProDy Overview and Applications (PDF, video) |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-16:00 | ProDy Tutorial; NMWiz Tutorial (PDF, video) |
| Coffee Break | |
| 16:15-18:00 |
Participant tutorial options: |
Fri, June 14: Druggability Simulations, and Analyzing Sequence Patterns and Structural Dynamics - Ivet Bahar and Ahmet Bakan
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Druggability: Method and Applications (PDF, video) |
| Coffee Break | |
| 10:50-12:00 | Comparative Analysis of Sequence Patterns and Structural Dynamics for Families/Ensembles of Proteins (PDF, video) |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 13:30-15:00 | Druggability Tutorial; Evol Tutorial |
Tutorial Options:
* Expert NAMD Set Tutorials:
- Shape-Based Coarse Graining
- User-Defined Forces in NAMD
Click here to see descriptions of tutorials listed in program.
Note: participants may also download and get assistance with other tutorials from the TCBG tutorials website during the workshop.
Program subject to change. Workshop supported by NIH 9P41GM104601 "Center for Macromolecular Modeling and Bioinformatics", and NIH P41 GM103712 "NIH Center for Multiscale Modeling of Biological Systems".