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:
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 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:
1) ENM Analysis
2) Ensemble Analysis
3) Structure Analysis
4) Trajectory Analysis
5) Conformational Sampling

 

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".

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