Aug 29, 2024
Protein structure prediction with AlphaFold-Multimer
- 1Sascha Martens lab, University of Vienna, Max Perutz Labs - Vienna
Protocol Citation: Elias Adriaenssens 2024. Protein structure prediction with AlphaFold-Multimer. protocols.io https://dx.doi.org/10.17504/protocols.io.81wgbz25qgpk/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: 103957
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 describes the protein structure prediction with AlphaFold-Multimer.
Protein sequences were downloaded from the Uniprot server.
A locally installed version of AlphaFold-Multimer was used for structure prediction with 5 models per prediction followed by Amber relaxation.
Interaction scores (ipDT) 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.