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

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.