Computational Biophysics Workshop

Program

Mon, Aug 4: Introduction to Protein Structure and Dynamics - Klaus Schulten

07:30-09:00 Registration Breakfast
09:00-09:10 Opening Remarks
09:10-10:40 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, Aug 5: Statistical Mechanics of Proteins - Klaus Schulten

07:30-09:00 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: User Defined Forces in NAMD; Shape-Based Coarse Graining

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: User Defined Forces in NAMD; Shape-Based Coarse Graining

 

Wed, Aug 6: Force Field Parameterization - Emad Tajkhorshid

07:30-09:00 Breakfast
09:00-10:30 Introduction to Topology, Parameters, and Structure Files
Coffee Break  
10:50-12:00 Topology, Parameters, and Structure Files
12:00-12:20 Q & A
Lunch Break  
14:00-16:00 Parameterizing a Novel Residue; Topology File Tutorial
Coffee Break  
16:15-18:00

Parameterizing a Novel Residue; Topology File Tutorial

- Participant tutorial options: NAMD Tutorial & Stretching Deca-alanine

 

Thu, Aug 7: Simulating Membrane Channels - Emad Tajkhorshid

07:30-09:00 Breakfast
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 Membrane Proteins Tutorial; Simulation of Water Permeation through Nanotubes
Coffee Break  
16:15-18:00 Membrane Proteins Tutorial; Simulation of Water Permeation through Nanotubes

 

Fri, Aug 8: Introduction to Bioinformatics - Zaida Luthey-Schulten

07:30-09:00 Breakfast
09:00-10:30 Part I - Introduction to Evolutionary Concepts and VMD/MultiSeq
Part II - Applications of MultiSeq Evolution of Translation: Dynamics of Recognition in RNA:Protein Complexes
Coffee Break  
10:50-12:00 Part III - Towards in silico Cells: Simulating Processes in Entire Cells
12:00-12:30 Q & A; Group picture
Lunch Break  
14:00-16:00

Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or
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,
Dynamical Network Analysis, or
Participants work on their own projects

Coffee Break  
16:15-18:00 Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or
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,
Dynamical Network Analysis, or
Participants work on their own projects

Click here to see descriptions of tutorials listed in program.

Note: program subject to change. Workshop supported by NIH 9P41GM104601 "Center for Macromolecular Modeling and Bioinformatics".