ACES: AlphaFold Protein Structure Prediction
Overview
Instructor(s): Dr. Michael Dickens
Time: Tuesday, April 8, 2025 — 1:30PM-4:00PM CT
Location: Online using Zoom
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills
This short course covers how to run AlphaFold on the ACES cluster, utilizing the NVIDIA H100 GPUs.
Course Materials
Presentation slides
The presentation slides will be made 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
- Learn how to run ParaFold to reduce GPU idle time
- Submit an example ParaFold/AlphaFold2 job script
- Submit an example AlphaFold3 job script
- Visualize the AlphaFold job results
This course focuses, among others, on the following topics:
- AlphaFold History
- Running AlphaFold2 on ACES
- ParaFold AlphaFold2 workflow
- AlphaFold2 with reduced_dbs
- AlphaFold2 confidence metrics
- Running AlphaFold3 on ACES
- HPRC Cluster Utilities
- Visualization of Results
- view predictions in Jmol
- Job Resource Monitoring
Note: During the class sessions many aspects of the material will be illustrated live via a login to ACES. Attendees will follow along and complete the exercises on their own computer.
You are encouraged to contact the HPRC helpdesk with any questions regarding ACES.