Computational Biophysics Workshop - Pittsburgh, May 19-23, 2014

Program

Locations:
  • Pittsburgh Supercomputing Center, 300 S. Craig St., Pittsburgh, PA - in the Oakland neighborhood of Pittsburgh (map)
  • Lectures will be held in Room #103
  • Tutorial sessions will be held in Room #110
  • Meals will be served in Room #102

Mon, May 19: 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
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, May 20: 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
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, 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, May 21: Computational Nano-Bio - Alek Aksimentiev

08:30-09:00 Continental Breakfast
09:00-10:30 Introduction to Modeling and Simulations of Nucleic Acid Systems
Coffee Break  
10:50-12:00 Modeling the Interface Between Biological and Synthetic Materials
12:00-12:20 Q & A
Lunch Break  
14:00-16:30

Modeling Nanopores for Sequencing DNA
Coffee Break  
16:45-18:00 Introduction to MD Simulations of DNA-protein systems

Thu, May 22: 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 of Biomolecular Systems using ProDy
Coffee Break  
10:50-12:00 ProDy Overview and Applications
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, May 23: Druggability Simulations, and Analyzing Sequence Patterns and Structural Dynamics - Ivet Bahar and Chakra Chennubhotla

08:30-09:00 Continental Breakfast
09:00-09:30 Druggability: Method
09:00-10:30 Druggability: Applications in ProDy
Coffee Break  
10:50-11:20 Comparative Analysis of Sequence Patterns and Structural Dynamics for Families/Ensembles of Proteins
11:20-12:30 Comparative Sequence Analysis in ProDy
Lunch Break  
13:30-15:00 Druggability and Evol Tutorials in ProDy
Coffee Break  
16:15-18:00 Tutorial options

 

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".