Computational Biophysics Workshop - Pittsburgh, Nov. 6-9, 2006

TCB Hands-on Workshop in Pittsburgh

Program

Locations: 

  • Lectures: 1018 Biomedical Science Tower 3

  • Labs: 1047 (1048/1049) Biomedical Science Tower 3

Mon, 11/6: Introduction to Protein Structure and Dynamics, K. Schulten

08:30-09:00 Breakfast
09:00-09:15 Opening Remarks
09:15-10:00 Molecular Dynamics Method
10:00-10:45 Molecular Dynamics with NAMD
Coffee Break
11:00-11:50 Equilibrium Properties of Proteins
11:50-12:00 Daily Q & A
Lunch Break
14:00-14:15 Overview of Hands-on Sessions
14:15-15:30 Molecular Dynamics/NAMD Tutorial
Coffee Break
15:45-18:00 Molecular Dynamics/NAMD Tutorial  (continued)
 

Tue, 11/7: Parameters for Classical Force Fields, K. Schulten & E. Tajkhorshid

08:30-09:00 Breakfast
09:00-10:00 Nonequilibrium Properties of Proteins
10:00-10:40 Classical Force Fields
Coffee Break
11:00-11:50 Force Fields Parameterization
11:50-12:00
 		 Daily Q & A
Group photo
Lunch Break
14:00-16:00 Molecular Dynamics/NAMD Tutorial  (continued)
Coffee Break
16:15-18:00 Topology Files, Parameterization of a Novel Residue Tutorials

 

Wed, 11/8: Introduction to Bioinformatics, Z. Luthey-Schulten

08:30-09:00 Breakfast
09:00-10:00 Introduction to Bioinformatics: Sequence, Structure, and Alignment
10:00-10:40 Evolutionary Concepts in Bioinformatics
Coffee Break
11:00-11:50 Application of Bioinformatics
11:50-12:00 Daily Q & A
Lunch Break
14:00-16:30 Evolution of Protein Structure - Aspartyl tRNA Synthetase
Coffee Break
16:45-18:00 Evolution of Protein Structure - Aspartyl tRNA Synthetase (continued)
 

Thu, 11/9: Simulating Membrane Channels, E. Tajkhorshid

08:00-08:30 Breakfast
08:30-09:00 Introduction and Examples
09:00-10:00 Transport in Aquaporins
Coffee Break
10:10-10:50 Nanotubes
10:50-11:00 Daily Q&A
Lunch Break
14:00-15:30 Nanotubes/IMD
Coffee Break
15:45-18:00 Stretching Deca-alanine/Open tutorial work time