Comment on Protein folding is not solved yet
ranzispa@mander.xyz 6 days agoNot solved, no. Definitely much much better than before. The difference AlphaFold made is significant: we’re talking about getting a decent model in a couple minutes using a PC compared to several months of calculations before.
However we still need experimental data: in many occasions AlphaFold gives an incorrect model. With some experimental data that model can be improved, but we still have no reliable way to know what the structure of a protein is starting from the amino acidic sequence without extensive experimentation.
That’s the big promise of quantum computers, there are however two major problems in my opinion:
That’s really intereting. Thank you for the informative comment.
I once did a internship where we solved protein structures by using Cristalisation and X-ray fracturing. Is this what you’re referring to with extensive research or has the methodology advanced?
Yes, X-ray is the gold standard. Technology has advanced in the sense that the protein crystallization is now more standardized and automated, as well as the analysis of the results.
It is not the only technique, for example there are cheaper ones based on mass spectrometry which do not resolve the full structure but allow to understand which amino acids are spatially near; such information is useful when developing a protein model and to validate whether a model is plausible.
The other two major techniques for structure resolution are NMR spectra analysis and the fairly novel technique of cryo electro microscopy.
These in general do not resolve the protein structure to the same resolution as X-ray but have other advantages: they allow you to observe the protein structure when in solution, which may be significantly different from the crystallized structure.
Thank you ❤️
Didn’t google shut down alphafold recently?
MonkderVierte@lemmy.zip 6 days ago
90% of quantum computing is a hype scam anyway.
ranzispa@mander.xyz 6 days ago
Agreed, I still do hope they can maintain some of their promises. However until now, I have not really seen any real advances towards making something useful.
I do not have a deep knowledge of quantum computers, but I know plenty people working on them and often get to talk about it.
I know people working on chemical problems who are basically approximating atoms to point charges. And either way those calculations are slower than on a CPU. For the uninformed, in chemistry the interactions between electronic orbitals is fundamental; this is in no way an approximation useful to obtain any kind of information.
This is fine, I understand methodologies take time to develop; however as far as I understand it those techniques they’re using are mathematically limited to using point charges: no matter how much they improve them that’ll be the highest level of accuracy.
I hope someone finds a way to handle such things better: as much as you can make a great machine learning model you’re always depending on available data.