Computational Biophysics Workshop - Urbana, Nov. 18-22, 2013


Lectures

  • 11/18: Introduction to Protein Structure and Dynamics - Klaus Schulten
    • Structure and Sequence Analysis with VMD (pdf)
    • Introduction to Molecular Dynamics with NAMD (pdf)
    • NAMD from the Developer's Perspective - Jim Phillips (pdf)

  • 11/19: Force Field Parameterization - Emad Tajkhorshid
    • Introduction to Topology, Parameters, and Structure Files (pdf)
    • Topology, Parameters, and Structure Files (pdf)
    • Force Field Toolkit (ffTK) - Chris Mayne (pdf)

  • 11/20: Computational Nano-Bio - Alek Aksimentiev
    • Introduction to Modeling and Simulations of Nucleic Acid Systems (pdf)
    • Modeling the Interface Between Biological and Synthetic Materials (pdf)

  • 11/21: Introduction to Bioinformatics - Zaida Luthey-Schulten
    • Part I - Introduction to Evolutionary Concepts and VMD/MultiSeq (pdf)
    • Part II - Applications of MultiSeq Evolution of Translation: Dynamics of Recognition in RNA:Protein Complexes (pdf)
    • Part III - Towards in silico Cells: Simulating Processes in Entire Cells (pdf)
    • VMD from the Developer's Perspective - Barry Isralewitz (pdf)

  • 11/22: Simulating Membrane Channels - Emad Tajkhorshid
    • Introduction and Examples (pdf)
    • Transport in Aquaporins; Nanotubes (pdf)