Computational Biophysics Workshop - Champaign, Aug. 10-14, 2009
Lectures
- Mon, 8/10: Introduction to Protein Structure and
Dynamics, K. Schulten
- Opening Remarks (pdf)
- Structure and Sequence Analysis with VMD (pdf, pdf)
- Introduction to Molecular Dynamics with NAMD (pdf)
- VMD 1.8.7 - Key features of recent release (John Stone) (pdf)
- Tue, 8/11: Statistical
Mechanics
of Proteins, K. Schulten
- Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD (pdf, pdf, pdf)
- Exemplary Applications of VMD / NAMD in Modern Research (pdf)
- NAMD 2.7 - Key features of upcoming release (Chris Harrison) (pdf)
- Wed, 8/12: Introduction to Bioinformatics, Z.
Luthey-Schulten
- Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD (pdf)
- Application of MultiSeq to Evolution of Translation Machinery (pdf)
- Sequence analysis in VMD 1.8.7 - Key features (Kirby Vandivort) (pdf)
- Thu, 8/13: Parameters
for
Classical Force
Fields, E. Tajkhorshid
- Introduction to Topology, Parameters, and Structure Files (pdf)
- Examples and Applications (pdf)
- GPU accelerated NAMD 2.7 (Jim Phillips)
(pdf)
- Fri, 8/14: Simulating Membrane Channels, E. Tajkhorshid
