AlphaFold Protein Structure Prediction
Overview
Instructor: Michael Dickens
Time: Friday, February 23, 2024 — 1:30PM-4:00PM CT
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.
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 will follow along and complete the exercises on 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.