AlphaFold and friends on the HPC

AlphaFold
Introduction to AlphaFold
DeepMind
Critical Assessment of protein Structure Prediction (CASP)
The AlphaFold pipeline
Overview of the architecture
AlphaFold training details
Online accessibility
Publications, GitHub code and database
Official AlphaFold colab
ColabFold
AlphaFold on the HPC
Requirements to use the HPC
Basic UNIX commands
Prepare directories and files
Setting up the job script
AlphaFold outputs
Computational limits
Basic workflow example (ssh)
Basic workflow example (web interface)
Troubleshooting
Extra: AlphaFold-Multimer
VIBFold on the HPC
VIBFold: an adapted AlphaFold script
Instructions for running VIBFold
Overview of VIBFold outputs
AlphaPulldown on the HPC
Introduction
Instructions for running AlphaPulldown
RoseTTAFold
The RoseTTAFold pipeline
Online Accessiblity
Exercises
VIB Training Session (AlphaFold)
HPC: A first AlphaFold run
HPC: AlphaFold-Multimer
HPC: Generate PAE/PLDDT/MSA plots
HPC: Analyze the predicted SarsCoV2-VHH.E complex
HPC: Run AlphaPulldown on the HPC
ChimeraX: Display AlphaFold predictions and error estimates using ChimeraX
AFDB: Analyze the prediction for USP7
Colab: ColabFold on Google Colab
ESM: Run ESMFold via web interface
(old) HPC: Analyze the predicted SarsCoV1-VHH.72 complex
Solutions
VIB Training Session (AlphaFold)
Analyze the prediction for USP7 on AlphaFoldDB (solutions)
Analyze the predicted SARS-CoV-2 + VHH-E complex (solutions)
(old) Analyze the predicted SARS-CoV-1 + VHH-72 complex (solutions)
Previous Topic
Next Topic

VIB Training Session (AlphaFold)

AlphaFold and friends on the HPC VIB Training Session (AlphaFold)

Welcome to the VIB training session related to AlphaFold. In this section, you can find the exercises.

The powerpoint presentation can be downloaded from here.

Interesting further readings:
https://blog.matteoferla.com/2022/10/move-aside-coip-westerns-colabfold-has.html

Lesson Content
0% Complete 0/10 Steps
Previous Topic
Back to Course
Next Topic