Computational Biophysics Workshop

TCB Hands-on Workshop in Urbana  

Lectures

 

Day 1: Introduction to Protein Structure and Dynamics, K. Schulten

  • Opening Remarks (pdf, 185k)
  • Structure and Sequence Analysis with VMD (pdf, 606k; pdf, 461k)
  • VMD for Structure Building and Dynamics Analysis (pdf, 792k)

Day 2: Statistical Mechanics of Proteins, K. Schulten

  • Molecular Dynamics with NAMD I (pdf, 792k; pdf, 362k)
  • Molecular Dynamics with NAMD II (pdf, 285k; pdf, 1.1M)

Day 3: Parameters for Classical Force Fields, E. Tajkhorshid

  • Introduction to Topology, Parameters, and Structure Files (pdf, 1.1M)
  • Examples and Applications (pdf, 1.1M)

Day 4: Simulating Membrane Channels, E. Tajkhorshid

  • Introduction and Examples (pdf, 5.0M)
  • Transport in Aquaporins; Nanotubes (pdf, 2.3M)

Day 5: Introduction to Bioinformatics, Z. Luthey-Schulten

  • Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD
  • Application of MultiSeq to Evolution of Translation Machinery
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