Agenda: Hands-on Workshop on Computational Biophysics 2015
Workshop details: Home Agenda Suggested readings Evaluations
Mon. June1: 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 (PDF, video) |
09:10-10:30 | Structure and Sequence Analysis with VMD (PDF, 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. June 2: 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 (PDF1, PDF2, video) | |
Coffee break | ||
10:50- 12:00 | Applications of VMD / NAMD in Modern Research (PDF1, PDF2, video) | |
12:00-12:30 | Q & A; Group picture | |
Lunch break | ||
14:00-16:00 |
Participant tutorial options: |
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Coffee break | ||
16:15-18:00 | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine 2) GPU Accelerated Molecular Dynamics and Visualization 3) Shape-Based Coarse Graining |
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Dinner break (note: participants are on their own for this meal) |
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19:00-21:00 | Presentations by workshop participants |
Wed. June 3: Introductions to Evolutionary Concepts, Network Analysis,and Cell Simulations - Zan Luthey-Schulten
08:30-09:00 | Continental breakfast |
09:00-10:30 | Applications of Evolutionary Algorithms and Network Analysis in MultiSeq/VMD to Translation (PDF, video) |
Coffee break | |
10:50-12:00 | Introduction to Simulations of Bacterial Cells (video) |
12:00-12:20 | Q & A |
Lunch break | |
14:00-18:00 | Participant tutorial options: 1) Evolution of Translation 2) Network Analysis 3) Lattice Microbe Simulations |
Thu. June 4: 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 using ANM Server and ProDy API (PDF, video) |
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 |
Coffee break | |
16:15-18:00 |
Participant tutorial options: |
Fri. June 5: Druggability Simulations and Sequence Evolution Patterns - Ivet Bahar, Indira Shrivastava, and Cihan Kaya
08:30-09:00 | Continental breakfast |
09:00-10:30 | Druggability: Methods and Applications using ProDy (PDF, video) |
Coffee break | |
10:50-12:00 | EVOL: Comparative Analysis of Sequence Evolution Patterns, Structure, and Dynamics (PDF, video) |
12:00-12:30 | Druggability tutorial using ProDy |
Lunch break | |
14:00-15:30 | Evol Tutorials in ProDy |
15:30-16:00 | Discussion and Closure |
Coffee break | |
16:30-18:00 | Additional tutorials (optional) |
Tutorials
Note: participants may also download and get assistance with other tutorials from the TCBG tutorials website 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".