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alphafold-tutorial-ismb-2023

Workshop Schedule

Note: Times are relative to the start and end times of the Tutorial

0:00:00 - 0:15:00 Introductory Lecture on the Protein Folding Problem and Artificial Intelligence Approach to the Solution

0:15:00 - 0:30:00 Introduction to the AlphaFold Tools and Database

0:30:00 - 0:45:00 Setting up Colaboratory Notebooks to run code with a free Gmail account

0:45:00 - 1:45:00 Hands On Activity

  • Introduction to the Data Set used
  • Introduction to the Compute Environment
  • Introduction to the Alphafold Command Line Parameters
  • View the Code in the Notebooks
  • Run Alphafold on Command Line or using the form —- NOTEBOOKS
  • Review Alphafold results (RELAXED vs RELAXED_GPU)
  • Download Alphafold results

1:45:00 - 2:00:00 Coffee Break

2:00:00 - 2:20:00 Introduction to PyMoL and other Protein Viewers (e.g. Cn3D)

2:20:00 - 2:30:00 Setting up PyMoL on your own machine

2:30:00 - 3:30:00 Hands On Activity

  • Loading files into PyMOL

  • Picking residues to highlight

  • Other options in PyMOL for examining the protein structure

  • What have we learned from the visualizations?

  • What other questions might we ask?

3:30:00 - 3:45:00 Discussion session: How can this tool be applied to your research question? 3:45:00 - 4:00:00 Wrap up Lecture on Future Directions for AI and Resources for Further Study