Agenda: Hands-on Workshop on Computational Biophysics 2016

Mon. June 6: Introduction to Protein Structure and Dynamics - Juan 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 - Using VMD; NAMD Tutorial
  Coffee break
16:15-18:00 VMD Tutorial - Using VMD; NAMD Tutorial

 

Tue. June 7: Statistical Mechanics of Proteins - Juan Perilla

08:30-09:00 Continental breakfast
09:00-10:30 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD 
  Coffee break
10:50- 12:00 Applications of VMD / NAMD in Modern Research 
12:00-12:30 Q & A; Group picture
  Lunch break
14:00-16:00

Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine
2) GPU Accelerated Molecular Dynamics and Visualization
3) Shape-Based Coarse Graining

  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
  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
09:00-09:45 Essential statistical mechanics of trajectories: equilibrium and non-equilibrium perspectives
09:45-10:30 The weighted ensemble (WE) method: Basics and applications
  Coffee break
10:45-11:15 Advanced analysis of trajectories 
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

 

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".

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