Computational Biophysics Workshop - Urbana, Feb. 11-15, 2012
Lectures
- 2/11: Introduction to Protein Structure
and Dynamics - Klaus Schulten
- Opening Remarks (pdf)
- Structure and Sequence Analysis with VMD (pdf)
- Introduction to Molecular Dynamics with NAMD (pdf)
- 2/12: Statistical Mechanics of Proteins - Klaus Schulten
- Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD (pdf)
- Exemplary Applications of VMD / NAMD in Modern Research (pdf, pdf)
- 2/13: Parameters for Classical Force Fields - Emad Tajkhorshid, Christopher Mayne
- Introduction to Topology, Parameters, and Structure Files (pdf) - Tajkhorshid
- Examples and Applications (pdf) - Tajkhorshid
- A Brief Overview of the Force Field Toolkit (ffTK) (pdf, pdf) - Mayne
- 2/14: Simulating Membrane Channels - Emad Tajkhorshid
- Introduction and Examples (pdf)
- Transport in Aquaporins; Nanotubes (pdf)
- 2/15: Introduction to Bioinformatics - Zan Luthey-Schulten
- Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD (pdf, pdf) (audio lecture)
- Application of MultiSeq to Evolution of Translation Machinery (pdf)