AlphaFold Protein Structure Prediction

Overview

Instructor: Michael Dickens

Time: Friday, February 24, 2023 1:30PM-4:00PM CST

Location: Blocker 220

Prerequisites: Current HPRC account, Basic Linux/Unix skills

This short course covers how to run AlphaFold on the Grace cluster. It will also cover how to visualize protein structure prediction results using ChimeraX.

Course Materials

Presentation slides

The presentation slides are available as downloadable PDF files.

  • Alphafold Protein Structure Prediction (Fall 2022): PDF

Agenda

This course focuses, among others, on the following topics:

  • Resources and Limitations
  • Database Files
  • Running AlphaFold
    • Google Colab
    • ChimeraX + Google Colab
    • Grace GPU or non-GPU nodes
  • Visualization of Results
    • job resource usage
    • view predictions in ChimeraX
    • plotting pLDDT values
  • Alternative Workflows

Note: During the class sessions many aspects of the material will be illustrated live via a login to Grace. Attendees are welcome to follow these parts with their own laptops. They will need to configure their laptops to use the TAMULink wireless network. Relevant details on this can be found at: http://tamulink.tamu.edu/

You are encouraged to contact the HPRC helpdesk with any questions regarding Grace.