AlphaFold and friends on the HPC

AlphaFold
Introduction to AlphaFold
2 Topics
DeepMind
Critical Assessment of protein Structure Prediction (CASP)
The AlphaFold pipeline
2 Topics
Overview of the architecture
AlphaFold training details
Online accessibility
3 Topics
Publications, GitHub code and database
Official AlphaFold colab
ColabFold
AlphaFold on the HPC
9 Topics
Requirements to use the HPC
Basic UNIX commands
Prepare directories and files
Setting up the job script
AlphaFold outputs
Computational limits
Basic workflow example
Troubleshooting
Extra: AlphaFold-Multimer
VIBFold on the HPC
3 Topics
VIBFold: an adapted AlphaFold script
Instructions for running VIBFold
Overview of VIBFold outputs
RoseTTAFold
The RoseTTAFold pipeline
Online Accessiblity
RoseTTAFold on the HPC
Exercises
VIB Training Session (AlphaFold)
5 Topics
First experiment on the HPC
Analyze the prediction for USP7 on AlphaFoldDB
Run AlphaFold-Multimer
Generate PAE/PLDDT/MSA plots
Analyze the predicted SarsCoV1-VHH.72 complex
Solutions
VIB Training Session (AlphaFold)
2 Topics
Analyze the prediction for USP7 on AlphaFoldDB (solutions)
Analyze the predicted SarsCoV1-VHH.72 complex (solutions)
vib-logo
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AlphaFold on the HPC

AlphaFold and friends on the HPC AlphaFold on the HPC
Lesson Content
0% Complete 0/9 Steps
Requirements to use the HPC
Basic UNIX commands
Prepare directories and files
Setting up the job script
AlphaFold outputs
Computational limits
Basic workflow example
Troubleshooting
Extra: AlphaFold-Multimer
Previous Lesson
Back to Course
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