Computational Biophysics Workshop - Pittsburgh, May 16-20, 2011

TCB Hands-on Workshop in Pittsburgh

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, 5/16: Introduction to Protein Structure and Dynamics - Klaus Schulten

08:00-08:30 Registration and Continental Breakfast
08:30-09:00 Welcome and Brief Overview of the NRBSC - Markus Dittrich
09:00-09:10 Opening Remarks
09:10-10:40 Structure and Sequence Analysis with VMD
Coffee Break  
11:00-12:00 Introduction to Molecular Dynamics with NAMD
12:00-12:20 Q & A
Lunch Break  
13:30-14:00 Brief Overview of PSC - PSC Allocations Staff
14:00-16:00 VMD Tutorial - Using VMD; NAMD Tutorial
Coffee Break  
16:15-18:00 VMD Tutorial - Using VMD; NAMD Tutorial

 

Tue, 5/17: Statistical Mechanics of Proteins - Klaus Schulten

09:00-10:30 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD
Coffee Break  
10:50-12:00 Exemplary 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) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
Coffee Break  
16:15-18:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**

 

Wed, 5/18: Parameters for Classical Force Fields - Emad Tajkhorshid

09:00-10:30 Introduction to Topology, Parameters, and Structure Files
Coffee Break  
10:50-12:00 Examples and Applications
12:00-12:20 Q & A
Lunch Break  
14:00-16:30 Parameterizing a Novel Residue
Coffee Break  
16:45-18:00 Topology File Tutorial

 

Thu, 5/19: Simulating Membrane Channels - Emad Tajkhorshid

09:00-10:30 Introduction and Examples
Coffee Break  
10:50-12:00 Transport in Aquaporins; Nanotubes
12:00-12:20 Q & A
Lunch Break  
14:00 -16:00 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  
16:15-18:00 Participant tutorial options:
1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**

 

Fri, 5/20: Introduction to Bioinformatics - Zaida Luthey-Schulten

09:00-10:30 Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD
Coffee Break  
10:50-12:00 Application of MultiSeq to Evolution of Translation Machinery
12:00-12:20 Q & A
Lunch Break  
14:00-16:00 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  
16:15-18:00 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

 

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. Workshop supported in part by NIH P41-RR005969 "Resource for Macromolecular Modeling and Bioinformatics".