ACES: AlphaFold Protein Structure Prediction
Overview
Instructor: Michael Dickens
Time: Tuesday, October 1, 2024 — 1:30PM-4:00PM CT
Location: Online using Zoom
Prerequisites: Current ACCESS ID, basic Linux/Unix skills
This short course covers how to run AlphaFold on the ACES cluster, utilizing the NVIDIA H100 GPUs.
Registration will open up on this webpage the week before the class.
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
- 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
- ACES GPU or non-GPU nodes
- Visualization of Results
- job resource usage
- plotting pLDDT values
- Alternative Workflows
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.