Aug 29, 2024
AlphaFold 3 screen
- 1Sascha Martens lab, University of Vienna, Max Perutz Labs - Vienna
Protocol Citation: Elias Adriaenssens 2024. AlphaFold 3 screen. protocols.io https://dx.doi.org/10.17504/protocols.io.6qpvr8rm2lmk/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 22, 2024
Last Modified: August 29, 2024
Protocol Integer ID: 103958
Keywords: ASAPCRN
Funders Acknowledgement:
Aligning Science Across Parkinson’s (ASAP)
Grant ID: ASAP-000350
Marie Skłodowska-Curie MSCA Postdoctoral fellowship
Grant ID: 101062916
Abstract
This protocol is about the AlphaFold 3 screen.
Protein sequences were downloaded from the Uniprot server.
We accessed AlphaFold 3 from its virtual server (https://alphafoldserver.com) to run pairwise predictions with 5 models per prediction.
Predictions with an ipTM score of > 0.5 were considered putative hits and diagnostic plots (PAE plot and pLDDT plot) as well as the generated structures were manually inspected.
Predicted structures were visualized with ChimeraX-1.8.