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AlphaFold on Rivanna

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

AlphaFold on Rivanna

This workshop will cover:

Introduction to GPU Computing
Introduction to AlphaFold
Running AlphaFold on Rivanna

Last updated on Jan 1, 0001

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