End-to-end differentiable learning of protein structure

[nabla9]

It would be cool if machine learning researchers would start participating CASP and CAPRI. If you crack Go, you get fame, but if you crack protein prediction, you get Nobel price and completely revolutionize biochemistry and medicine.

http://predictioncenter.org/

http://www.ebi.ac.uk/msd-srv/capri/

edit: Why there is no XPRICE for protein folding?

[cing]

DeepMind and others are trying. "Hassabis said the company is now planning to apply an algorithm based on AlphaGo Zero to other domains with real-world applications, starting with protein folding."

[1] https://www.bloomberg.com/news/articles/2017-10-18/deepmind-...

[matt4077]

I used to work on protein structure about ten years ago.

Back then, the mood kind of changed from “solve this and you have a Nobel waiting”: the general opinion was that progress was both significant and piecemeal, making it unlikely a Nobel will be awarded because “cracking it”would end up being to hard to assign to any three people.

[mathperson]

lol what-I was looking at this list of people who do this-in fact a lot of them ARE machine learning researchers...including some in my department!

[sjg007]

It's happening.

[RivieraKid]

I would guess that there have been many attempts to use ML for protein folding. It's one of the most obvious ways to approach the problem.

[dr_coffee]

I work on protein structure, albeit not from a computational standpoint, and it struck me as odd that none of the work from the Baker group (Univ Washington) e.g. Rosetta (https://www.rosettacommons.org/) was mentioned. Rosetta can be used to predict tertiary structure from amino acid sequence. Does anyone familiar with the field know how the methods used by software like ROSETTA differ from those presented in this paper?

[superfx]

Hi! I’m the author of the paper. Not sure why you say Rosetta isn’t mentioned? It’s extensively referenced throughout the paper, discussed in the discussion section, and is one of the top 5 CASP servers compared to in the results section.

Also as for how it’s different from what’s described in the paper, that’s the topic of the introduction of the paper. Rosetta uses both fragment assembly and co-evolution methods.

[sungam]

This is a very interesting approach. Clearly a lot more work to do but the robust prediction of protein structure from sequence would be an absolute game changer for biomedical science so I hope that this opens up new strategies.

[RivieraKid]

What are the real-world applications of protein folding (preferably, some specific example)? I always hear that it's really important for drug design and biotechnology but have a hard time imagining something concrete.

[superfx]

Re drug discovery, often times in “rational” drug design, medicinal chemists try to make small molecules that bind snuggly into a binding pocket on the protein. Having the structure of the protein aids greatly in that process.

[resiros]

Cool method! Are you planning to participate in the next CASP? Do you plan to open source the code?

[superfx]

Yes! Certainly on the source code, and hopefully on CASP13 too.