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.

A Registration button will appear here when registration has been opened.

Course Materials

Presentation slides

The presentation slides will be made available as downloadable PDF files.

  • AlphaFold Protein Structure Prediction (Spring 2025): PDF

  • AlphaFold Protein Structure Prediction (Fall 2024): PDF
  • AlphaFold Protein Structure Prediction (Spring 2024): PDF

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.