Agenda: Hands-on Workshop on Computational Biophysics 2014
Workshop details: Homepage
Mon, May 19: 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 |
| 09:00-09:10 | Opening Remarks (video) |
| 09:10-10:30 | Structure and Sequence Analysis with VMD (PDF, video, video) |
| Coffee Break | |
| 10:50-12:00 | Introduction to Molecular Dynamics with NAMD (PDF, video) |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-16:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
| Coffee Break | |
| 16:15-18:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Tue, May 20: Statistical Mechanics of Proteins - Klaus Schulten
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD (PDF) |
| Coffee Break | |
| 10:50- 12:00 | Applications of VMD / NAMD in Modern Research (PDF, video) |
| 12:00-12:30 | Q & A; Group picture |
| Lunch Break | |
| 14:00-16:00 |
Participant tutorial options: |
| Coffee Break | |
| 16:15-18:00 | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine, or 2) GPU Accelerated Molecular Dynamics and Visualization, or 3) Shape-Based Coarse Graining |
| Dinner Break |
(note: participants are on their own for this meal) |
| 19:00-21:00 | Presentations by workshop participants |
Wed, May 21: Computational Nano-Bio - Alek Aksimentiev
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Introduction to Modeling and Simulations of Nucleic Acid Systems (PDF, video) |
| Coffee Break | |
| 10:50-12:00 | Modeling the Interface Between Biological and Synthetic Materials (PDF, video) |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-16:30 | Modeling Nanopores for Sequencing DNA; Introduction to MD Simulation of DNA-protein Systems |
| Coffee Break | |
| 16:45-18:00 | Modeling Nanopores for Sequencing DNA; Introduction to MD Simulation of DNA-protein Systems; |
Thu, May 22: Collective Dynamics of Proteins Using Elastic Network Models - Ivet Bahar, Tim Lezon and Chakra Chennubhotla
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Elastic Network Models (ENMs) and Collective Motions of Biomolecular Systems using ProDy (video) |
| Coffee Break | |
| 10:50-12:00 | ProDy Overview and Applications (PDF) |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-16:00 | ProDy Tutorial; NMWiz Tutorial |
| Coffee Break | |
| 16:15-18:00 |
Participant tutorial options: |
Fri, May 23: Druggability Simulations and Sequence Evolution Patterns - Ivet Bahar, Indira Shrivastava, and Chakra Chennubhotla
| 08:30-09:00 | Continental Breakfast |
| 09:00-09:30 | Druggability: Method (PDF, video) |
| 09:30-10:30 | Druggability: Applications in ProDy |
| Coffee Break | |
| 10:50-11:20 | Comparative Analysis of Sequence Patterns and Structural Dynamics for Families/Ensembles of Proteins (PDF, video) |
| 11:20-12:30 | Comparative Sequence Analysis in ProDy |
| Lunch Break | |
| 13:30-15:00 | Druggability and Evol Tutorials in ProDy |
| Coffee Break | |
| 16:15-18:00 | Tutorial options |
Tutorials
Note: participants may also download and get assistance with other tutorials from the TCBG tutorials website, the Aksimentiev group tutorial pages and the ProDy 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".