Computational Biophysics Workshop

Lectures

  • Mon, 11/1: Introduction to Protein Structure and Dynamics, K. Schulten 
    • Opening Remarks (pdf)
    • Structure and Sequence Analysis with VMD (pdf)
    • Introduction to Molecular Dynamics with NAMD (pdf)

  • Tue, 11/2: Statistical Mechanics of Proteins, K. Schulten and C. Chipot 
    • Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD - K. Schulten (pdf, pdf)
    • Good Practices in Free Energy Calculations - C. Chipot (pdf)

  • Wed, 11/3: Introduction to Bioinformatics, Z. Luthey-Schulten
    •  Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD
    • Application of MultiSeq to Evolution of Translation Machinery

  • Thu, 11/4: Parameters for Classical Force Fields, E. Tajkhorshid
    • Introduction to Topology, Parameters, and Structure Files (pdf)
    • Examples and Applications (pdf)

  • Fri, 11/5: Simulating Membrane Channels, E. Tajkhorshid
    • Introduction and Examples (pdf)
    • Nanotubes (pdf)
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