AlphaFold Protein Structure Prediction
Overview
Instructor: Michael Dickens
Time: Friday, October 25, 2024 — 1:30PM-4:00PM CT
Location: Blocker 220
Prerequisites: Active 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.
Learning Objectives and Agenda
In this class, participants will:
- Learn about AlphaFold resources and Limitations
- Learn about shared database files
- Submit an example AlphaFold job script
- Visualize the AlphaFold job results
- Learn how to run ParaFold to reduce GPU idle time
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.
You are encouraged to contact the HPRC helpdesk with any questions regarding Grace.