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
If we knew:

(a) the structure of every protein (what DeepMind is doing here)

(b) how different protein structures interact (i.e. protein complexes - DeepMind is working on this but not there yet)

Then we could use those two building blocks to design new proteins (drugs) that do what we want. If we solve those two problems with very high accuracy, we can also reduce the time it takes to go from starting a drug discovery programme to approved medicine.

Obtaining all protein structures and determining how they interact is a key step towards making biology more predictable. Previously, solving the structure of a protein was very time consuming. As a result, we didn’t know the structure for a majority of proteins. Now that it’s much faster, downstream research can move faster.

Caveat: we should remember that these are all computational predictions. AlphaFold’s predictions can be wrong and protein structures will still need to be validated. Having said that, lots of validation has already occurred and confidence in the predictions grows with every new iteration of AlphaFold.

>>axg11+D9
How are the predictions validated? Waiting for the old fashioned way for... very difficult crystal structure experiments? Or something else?

>>lamena+jf
If the predictions are generally good enough, could also skip the validation and directly try to get a desired effect or reaction. That isn't strictly speaking validating the structure, but depending on the use case might be easier to just go for an outcome - really a question of application and cost efficiency.

>>Random+Pi
I mean nothing is stopping you from skipping validation with pre-alphafold techniques and say for drug discovery to already do drug screening using the predicted structure. It's just the drug screening software is already error prone so you are still going to have to do some validation. However having an idea on a potential structure means that you can do other techniques that are simpler to validate it that are less expensive/time consuming (I'm thinking of things similar to FRET).

Another idea is these may come into play for anti-verification, so if you are drug screening against a known structure. You could potentially use these more flawed structures of proteins you don't want to target but may be similar, and try to reduce the drug's efficacy at binding them. Or something to that effect. All of that is fun ideas that are currently being explored in that space but we'll see where it takes us.