Computational Biophysics Workshop - Lake Tahoe, May 23-27, 2005

TCB Hands-on Workshop in Lake Tahoe

Program

Locations: 

  • All workshops are held in the Mountain Room/Squaw Peak of the Conference Center

  • Breakfast and lunch are in Granhall

  • Refreshment breaks are provided in the 'pre-function' area just outside of the workshop room

  • Dinner is in Alumni Room Monday-Thursday, and Cedar House on Friday

Mon, 5/23: Introduction to Protein Structure and Dynamics, K. Schulten

07:30-09:00 Breakfast
09:00-09:30 Opening Remarks
09:30-10:40 Molecular Graphics Perspective of Protein Structure and Function
Coffee Break
11:00-11:50 Molecular Dynamics Method
11:50-12:00 Daily Q & A
Lunch Break
19:00-19:45 Overview of Hands-on Sessions  
20:00-20:30 Molecular Graphics Tutorial
Coffee Break
20:45-23:00 Molecular Graphics Tutorial (continued)
 

Tue, 5/24: Introduction to Bioinformatics, Z. Luthey-Schulten

07:30-09:00 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
19:00-19:30 Evolution of Protein Structure - Aspartyl tRNA Synthetase
Coffee Break
19:45-21:00 Evolution of Protein Structure - Aspartyl tRNA Synthetase (continued)
21:00-23:00 Sequence Alignment Algorhithms/Bioinformatics Study of Aquaporins


Wed, 5/25: Statistical Mechanics of Proteins, K. Schulten

07:30-09:00 Breakfast
09:00-10:00 Molecular Dynamics with NAMD
10:00-10:40 Equilibrium Properties of Proteins
Coffee Break
11:00-11:50 Nonequilibrium Properties of Proteins
11:50-12:00 Daily Q & A
Lunch Break
19:00-20:30 Molecular Dynamics Tutorial
Coffee Break
20:45-23:00 Molecular Dynamics Tutorial (continued)
 

Thu, 5/26: Parameters for Classical Force Fields, E. Tajkhorshid

07:30-09:00 Breakfast
09:00-10:00 Introduction to Classical Force Fields
10:00-10:40 Force Fields Parameterization
Coffee Break
11:00-11:50 Applications
11:50-12:00 Daily Q&A
Lunch Break
19:00-20:30 Paramaterizing a Novel Residue
Coffee Break
20:45-23:00 Topology File Tutorial
 

Fri, 5/27: Simulating Membrane Channels, E. Tajkhorshid

07:30-09:00 Breakfast
09:00-10:00 Introduction and Examples
10:00-10:40 Transport in Aquaporins
Coffee Break
11:00-11:50 Nanotubes
11:50-12:00 Daily Q&A
Lunch Break
19:00-20:00 Nanotubes
20:00-20:30 Steered Molecular Dynamics Tutorial
Coffee Break
20:45-23:00 Steered Molecular Dynamics Tutorial (continued)