Computational Biophysics Workshop - Atlanta, Mar. 21-25, 2011

Program

Location:
  • Conference Room 102, Pettit Building

3/21: Introduction to Protein Structure and Dynamics - Klaus Schulten, Jeff Skolnick

08:00-08:30 Participant Registration
08:30-08:40 Opening Remarks, Steve Harvey, Klaus Schulten
08:40-10:10 Introduction to Molecular Dynamics with VMD & NAMD, Klaus Schulten
Coffee Break  
10:30-12:00 From Molecules to Cells - Whole Cell Simulations, Jeff Skolnick, CSSB
12:00-12:20 Q & A
Lunch Break
13:20-15:00 VMD Tutorial - Using VMD; NAMD Tutorial
Coffee Break  
15:20-17:00 VMD Tutorial - Using VMD; NAMD Tutorial

 

3/22: Statistical Mechanics of Proteins - Klaus Schulten

08:30-10:00 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD
Coffee Break  
10:20-11:50 Exemplary Applications of VMD / NAMD in Modern Research
11:50-12:10 Q & A; Group picture
Lunch Break  
13:10-15:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
Coffee Break  
15:20-17:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**

 

3/23: Introduction to Bioinformatics - Zaida Luthey-Schulten

08:30-10:00 Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD
Coffee Break  
10:20-11:40 Application of MultiSeq to Evolution of Translation Machinery
11:40-12:00 Q & A
Lunch Break  
13:00-15:00 Participant tutorial options:
1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or
2) Expert Sequence Analysis
     - Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes
     - Evolution of Translation EF-Tu: tRNA
     - Evolution of Translation: The Ribosome; or
3) Participants work on their own projects
Coffee Break  
15:20-17:00 Participant tutorial options:
1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or
2) Expert Sequence Analysis
     - Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes
     - Evolution of Translation EF-Tu: tRNA
     - Evolution of Translation: The Ribosome; or
3) Participants work on their own projects

 

3/24: Parameters for Classical Force Fields - Emad Tajkhorshid

08:30-10:00 Introduction to Topology, Parameters, and Structure Files
Coffee Break  
10:20-11:40 Examples and Applications
11:40-12:00 Q & A
Lunch Break  
13:00-15:00 Parameterizing a Novel Residue
Coffee Break  
15:20-17:00 Topology File Tutorial

 

3/25: Simulating Membrane Channels - Emad Tajkhorshid

08:30-10:00 Modeling and Molecular Dynamics of Cellular Processes
Coffee Break  
10:20-11:40 Nanotubes
11:40-12:00 Q & A
Lunch Break  
13:00-15:00 Participant tutorial options:
1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
Coffee Break  
15:20-17:00 Participant tutorial options:
1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**

 

Tutorial Options:
* Expert NAMD Set Tutorials:
     - Shape-Based Coarse Graining
     - User-Defined Forces in NAMD, or
** Free Energy Set Tutorials
     - A Tutorial to Set Up Alchemical Free Energy Perturbation Calculations in NAMD
     - A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD

Click here to see descriptions of tutorials listed in program.

Note: program subject to change.