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AlphaFold on HPC

CPU vs. GPU The Protein Folding Problem CASP Competitions

AlphaFold

Pipeline and Architecture Outputs Overview Confidence Metrics

Running AlphaFold On Rivanna

Logging on to OOD Desktop Building a Working Directory Building a conda Environment Alphafold Working Directory Input - FASTA File Submit a SLURM Job

Outputs

Sequence Coverage Plot Sequence Coverage Script pLDDT Plot PAE Plot CSV Outputs - alphapickle PDB Structure

Visualizing 3D Structures

Modify Visualization in VMD Change Background Color Exporting in VMD

Protein Structure Database

Limitations

Alternative Frameworks

Introduction

This section will cover:

CPU vs. GPU
The Protein Folding Problem
CASP Competitions
What is AlphaFold?
Pipeline and Architecture
Confidence Metrics

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Last updated on May 20, 2025

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