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:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) GPU Accelerated Molecular Dynamics and Visualization Tutorial, or
3) Expert NAMD: Shape-Based Coarse Graining, User-Defined Forces in NAMD

Coffee Break  
16:15-18:00

Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) GPU Accelerated Molecular Dynamics and Visualization Tutorial, or
3) Expert NAMD: Shape-Based Coarse Graining, User-Defined Forces in NAMD

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:
1) Evolution of Translation
2) Network Analysis
3) Lattice Microbe Simulations

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:
1) ENM Analysis
2) Ensemble Analysis
3) Structure Analysis
4) Trajectory Analysis
5) Conformational Sampling
6) Druggability Simulations
7) Evol Analysis

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".