zlacker

>>MindGo+(OP)
Can someone put AlphaFold's problem space into perspective for me?

Why is protein folding important? Theoretical importance? Can we do something with protein folding knowledge? If so, what?

I've been hearing about AlphaFold from the CS side. There they seem to focus on protein folding primarily as an interesting space to apply their CS efforts.

>>dalbas+l7
You are basically made of proteins, which are basically folded sequences of amino acids, proteins are molecular machines that are the fundamental building block of animals, plants, bacteria, fungi, viruses etc.

So yeah the applications are enormous, from medicine to better industrial chemical processes, from warfare to food manufacturing.

>>fabios+P7
> proteins are molecular machines

Does that imply proteins have some dynamics that need to be predicted too? I remember seeing animations of molecular machines that appeared to be "walking" inside the body - are those proteins or more complex structures?

>>jebark+Vo
Yes, very much so. Even for proteins that seems like they are just scaffolding for a catalytic centre can have important dynamics.

A classic example is haemoglobin, that 'just' binds to oxygen at the iron in the middle of the haem. Other binding sites remote from the oxygen binding one can bind to other molecules - notably carbon dioxide. The 'Bohr effect' mechanism is outlined here : https://en.wikipedia.org/wiki/Bohr_effect#Allosteric_interac...

Even at the lowest level, there is some evidence that ligand binding can affect the structure of the backbone of the protein. For example, peptide plane flipping https://en.wikipedia.org/wiki/Peptide_plane_flipping although I'm not sure where the research is on this nowadays.

>>gillea+ur
Fascinating. I'm a mathematician turned AI researcher by day. The more I learn about biology the more I feel that our human engineering (hard and soft) is trivially simple compared to what evolution has already created and left for us to study.

>>jebark+Mt
May career path took me from the very hard sciences to the biological ones. Though bio is experimentally trivial compared to the complexity of astrophysics, bio theory is millennia harder.

One of my favorite quotes about biology goes something like:

"An alien spaceship lands in your yard. You are kindly invited in to study and tour the ship. The technology is clearly billions of years more advanced than our own. Not decades more, not millennia more, not megayears more, but clearly gigayears more.

This is biology"

Sorry, can't find the exact quote and citation right now!