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.