AlphaFold Protein Structure Prediction
Overview
Instructor(s): Dr. Michael Dickens
Time: Friday, March 28, 2025 — 1:30PM-4:00PM CT
Location: Blocker 220
Prerequisite(s): 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.
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Course Materials
Participation
During the training, attendees are expected to log in to an HPRC cluster using their own computer and complete the instructor-led examples and exercises.
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:
- AlphaFold History
- Running AlphaFold2
- Grace ParaFold AlphaFold2 workflow
- AlphaFold2 with reduced_dbs
- AlphaFold2 confidence metrics
- Running AlphaFold3 on Grace
- HPRC Cluster Utilities
- Visualization of Results
- view predictions in ChimeraX
- Job Resource Monitoring