Computational Biophysics Workshop - Pittsburgh, June 6-10, 2016
Program
Mon, June 6:
Introduction to Protein Structure and Dynamics
Juan R. Perilla
08:00-08:30 | Registration and Continental Breakfast |
08:30-09:00 | Welcome and Brief Overview - Ivet Bahar |
09:00-09:10 | Opening Remarks |
09:10-10:30 | Structure and Sequence Analysis with VMD |
Coffee Break | |
10:50-12:00 | Introduction to Molecular Dynamics with NAMD |
12:00-12:20 | Q & A |
Lunch Break | |
14:00-16:00 | VMD Tutorial; QwikMD Tutorial; NAMD Tutorial |
Coffee Break | |
16:15-18:00 | VMD Tutorial; QwikMD Tutorial; NAMD Tutorial |
Tue, June 7:
Statistical Mechanics of Proteins
Juan R. Perilla
08:30-09:00 | Continental Breakfast |
09:00-10:30 | Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD (PDF1, PDF2) |
Coffee Break | |
10:50-12:00 | Applications of VMD / NAMD in Modern Research (PDF1, PDF2) |
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: |
Dinner Break | (note: participants are on their own for this meal) |
19:00-21:00 | Presentations by workshop participants |
Wed, June 8:
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 (PDF1, PDF2) | ||
Coffee Break | |||
10:50-12:00 | Introduction to Simulations of Bacterial Cells (PDF1, PDF2) | ||
12:00-12:20 | Q & A | ||
Lunch Break | |||
14:00-18:00 | Participant tutorial options: |
|
Thu, June 9:
Collective Dynamics of Proteins Using Elastic Network Models
Ivet Bahar, Cihan Kaya, and Karolina Mikulska-Ruminska
08:30-09:00 | Continental Breakfast |
09:00-10:30 | Elastic Network Models (ENMs) and Collective Motions using ANM Server and ProDy API (PDF1, PDF2) |
Coffee Break | |
10:50-12:00 | ProDy Overview and Applications |
12:00-12:20 | Q & A |
Lunch Break | |
14:00-16:00 | ProDy Tutorial |
Coffee Break | |
16:15-18:00 | Participant tutorial options: |
Fri, June 10:
Understanding the statistical mechanics of trajectories, the Weighted Ensemble simulation strategy, and the WESTPA package
Daniel M. Zuckerman with Adam Pratt, Ali Saglam, Justin Spiriti and Ernesto Suarez
08:30-09:00 | Continental Breakfast |
09:00-09:30 | Essential statistical mechanics of trajectories: equilibrium and non-equilibrium perspectives |
09:00-10:30 | The weighted ensemble (WE) method: Basics and applications |
Coffee Break | |
10:45-11:15 | The weighted ensemble (WE) method: Basics and applications |
11:15-11:45 | NAMD + WE example/tutorial |
Lunch Break | |
13:00-14:00 | Practicalities of WE and WESTPA simulation |
14:00-15:45 | Analysis of WESTPA data; advanced considerations |
Coffee Break | |
16:00-17:00 | Tentative: Ken Dill seminar - offsite |
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".