When submitting a manuscript with alphafold2-based predictions, what all should I provide as supplemental data?

I'm thinking the rank 1 model PDB and json file, and then for all of the models (5 in my case) the pae.png and plddt.png.

Would someone want to see more than this or less than this?

#AlphaFold #AlphaFold2 #StructurePredictions #DeepMind

Clearly, there is still much to learn about this corner of the dark genome defined by HEATR5 proteins and their co-factors.

#Biorxiv #Preprint #MembraneTraffic #DarkGenome #DarkProteome #RareDisease #AlphaFold #AlphaFold2 #ProteinPrediction #Golgi #Clathrin #CellBiology #biochemistry #Bioscience

Biochemical analysis revealed that Lft1 and Laa2 bind to Laa1 via the same interface. Following a suggestion by a colleague to try Alphafold2, we found that the two likely bind via a common mechanism, although the Lft1 interface is a little larger—something confirmed by our biochemical results.

#Alphafold #AlphaFold2 #ProteinPrediction

May be useful for anyone using #AlphaFold2 models. I wrote a short #Python script to quickly print out high confidence af2 models and filter out fragmentary sequences.

#bioinformatics #biochemistry #protein

https://github.com/arikat/alphaFilter

Andrea Thorn, Universität Hamburg: Are AI-assisted #CryoEM and #crystallography the future?

#AlphaFold2 is already replacing #Synchrotron measurements, so these become available for mor complicated experiments.

Central Dogma of Structural #Biology (slide on display)

#AUSPEX: diagnostic tool for graphical #DataAnalysis / detect ice-ring artefacts, https://thorn-lab.com/auspex/ in #MX crystallography

How to Solve the Protein Folding Problem: #AlphaFold2 | by Leonardo Castorina | Mar, 2023 | Towards Data Science

#AI

https://towardsdatascience.com/how-to-solve-the-protein-folding-problem-alphafold2-6c81faba670d