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Alphafold is an amazing tool, but please please please, don’t think it’s omniscient and just magically knows what proteins look like If you have a 2.5 slot on your laptop there are a lot of options for 4tb ssd's. Especially considering proteins with idrs or ones with a lack of similar templates.
A subreddit to discuss alphafold and protein/peptide research. I don't have much experience with alphafold, but in general putting a 3tb db on an external usb drive sounds like a nightmare Alphafold is helping researchers build models, but it can’t yet simply find all protein states
F@h has always focused on molecular dynamics, while rosetta@home (a boinc project) looked for protein structures and has been more supplanted by alphafold
F@h also open sources all its results and was probably used to train alphafold. But i'm not sure if this is more to do with lack of 'training' data for the ml? Alphafold is all nice and good and i was able to display the proteins as a 3d model in blender But how do you do really useful stuff like actually working with the structure in the raw data form (atom distance matrix)
I want to do phylogenetic comparisons with other proteins and basically analyze the substructures regarding electric charges and stuff like that I know this can be programmed. The problem with alphafold is it's trained on a limited set of known data, specifically annotated data where a large number of similar structures exist It sucks at predicting membrane proteins and some barrel proteins i fed it, as the active sites tend to be cocked up to the point where it can't fit known substrates.
Alphafold's ability to rapidly and accurately predict protein structures has accelerated research across various medical fields, enabling deeper understanding of disease mechanisms and facilitating drug discovery efforts
The alphafold github pages only discuss executing the program in google cloud, and the specs for their google cloud instance sound quite formidable I'm on the software & infrastructure side of things, so perhaps don't have the depth of the answer you're looking for, and would be happy to be corrected But as far as i understand from the scientists on our team is that it depends
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