World's top constraint solvers want to help out with COVID

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World's top constraint solvers want to help out with COVID

Postby ge0ffrey » Sun Mar 08, 2020 10:58 am

Hi all,

Protein folding is NP-hard, just like the Traveling Salesman Problem, Bin Packing, etc.
Mathematical optimization software (AKA constraint solvers) [1] have been working on ever improving algorithms for such problems for decades.
This software use algorithms such as metaheursitics (tabu search, simulated annealing, late acceptance), linear programming, constraint programming, genetic algorithms, GRASP, branch&bound, ...

The world's top constraint solvers want to help out with improving the algorithms for protein folding for COVID-19:
https://or.stackexchange.com/questions/3644/are-there-any-covid-19-coronavirus-related-optimization-problems-with-input-da
We want to crowd solve it (think Kaggle).

Can you help us out to get started?

What do we need?

    An output data file description. Ideally we can send that into folding@home for verification.



[1] https://en.wikipedia.org/wiki/List_of_o ... n_software
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Re: World's top constraint solvers want to help out with COV

Postby moritzgedig » Mon Mar 23, 2020 8:55 am

If those approaches are applicable at all, you would first have to find a way to map the problem.

F@H works in the time domain, not just finding one configuration but following the "landscape".
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Re: World's top constraint solvers want to help out with COV

Postby Jesse_V » Tue Mar 24, 2020 4:20 am

The goal isn't really what the final shape or interaction will be. Folding@home builds statistical maps of how likely it is that a protein or molecule will change into a particular shape, then from that shape it tries to find what other shape it can form and how likely are those, and so on. This builds a big map of the entire interactive process. For example, if I'm testing the molecules of a drug to see how they interact with the coronavirus, it's useful to see that 85% of the time the interactions might work along a particular path, but 15% of the time they go in a completely different direction. You need to be able to see that information to get a good understanding of how molecular interactions can happen in the real world. F@h is extremely optimized in building these kinds of maps and statistical pathways.

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Re: World's top constraint solvers want to help out with COV

Postby Tohya » Thu Apr 02, 2020 7:19 pm

https://twitter.com/foldingathome/statu ... 3412453378

Interested in helping us develop and enhance the F@h architecture? Come join the development team at our F@h Fireside Chat on Thursday, April 9th, 4-5pm EDT! To receive a Discord invite link, fill out this form: https://tinyurl.com/firesidedev
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