Computational Biophysics Workshop - Urbana, Nov. 8-12, 2004

TCB Hands-on Workshop in Urbana

Program

Location

Beckman Institute Room 5269

Workshop Agenda

Mon, 11/8: Introduction to Protein Structure and Dynamics 

09:15-09:40 Opening Remarks
09:45-10:40 Molecular Graphics Perspective of Protein Structure and Function
Break
10:50-11:50 Molecular Dynamics Method
11:50-12:00 Daily Q & A
Lunch
14:00-14:40 Overview of Hands-on Sessions (E. Villa, F. Khalili) 
14:45-18:00 Molecular Graphics Tutorial
(R. Braun, M. Gao)

Tue, 11/9: Introduction to Bioinformatics

09:00-10:00 Sequence structure and alignment
10:00-10:40 Evolution of Protein Structure
Break
11:00-11:50 Bioinformatics of tRNA Synthase
11:50-12:00 Daily Q & A
Lunch
14:00-16:00 Evolution of tRNA Synthetases
(P. O'Donoghue, J. Yu)

Wed, 11/10: Statistical Mechanics of Proteins

09:00-10:00 Equilibrium Properties of Proteins
10:00-10:40 Nonequilibrium Properties of Proteins
Break
11:00-11:50 Simulated Cooling of Proteins
11:50-12:00 Daily Q & A
Lunch
14:00-18:00 Molecular Dynamics Tutorial
(M. Dittrich, T. Isgro)

Thur, 11/11: Parameters for Classical Force Fields

09:00-10:00 Introduction and Examples
10:00-10:40 Introduction to Classical Force Fields
Break
11:00-11:50 Methods of Parametrization
11:50-12:00 Daily Q&A
Lunch
14:00-15:30 System set-up of HisH
(F. Khalili, C. Kanchanawarin)
15:30-18:00 Semiempirical Parameter Gerneration with Spartan
(F. Khalili, C. Kanchanawarin)

Fri, 11/12: Simulating Membrane Channels

09:00-10:00 Introduction and Examples
10:00-10:40 Transport in Aquaporins
Break
11:00-11:50 Nanotubes
11:50-12:00 Daily Q&A
Lunch
14:00-15:00 Bioinformatics of Aquaporins
15:00-18:00 Nanotubes 
(J. Cohen, D. Lu)