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.

Course Materials

Presentation slides

The presentation slides are available as downloadable PDF files.

• AlphaFold Protein Structure Prediction (Spring 2025): PDF

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• AlphaFold Protein Structure Prediction (Fall 2024): PDF
• AlphaFold Protein Structure Prediction (Spring 2024): PDF
• AlphaFold Protein Structure Prediction (Fall 2023): PDF
• AlphaFold Protein Structure Prediction (Spring 2023): PDF
• AlphaFold Protein Structure Prediction (Fall 2022): PDF

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

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.