Alphafold 2 question
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Dan Kolis
Jan 24, 2023, 12:59:52 PM1/24/23
to DIYbio
Hello all,
Some of 'my people' at a USA university have whatever open source for Alphafold2 running. The code name for this seems to be evolving as: AF2 which is pretty convenient I suppose.
I asked the linux-poker-at guy if it will have an API to allow a submission of a XYZ file of atoms and will answer back with a PDB or MOLE-X, ... whatever. He said: "Program doesn't do that". He said it has worked on 27K line items and failed on a few he is playing with that.
Does anybody know of a parallel effort for a GET or POST that generates some answer, or other stimulus / response thing for a folding problem that's not a lookupped thing ?
Regards,
Daniel B Kolis
I asked the linux-poker-at guy if it will have an API to allow a submission of a XYZ file of atoms and will answer back with a PDB or MOLE-X, ... whatever. He said: "Program doesn't do that". He said it has worked on 27K line items and failed on a few he is playing with that.
Does anybody know of a parallel effort for a GET or POST that generates some answer, or other stimulus / response thing for a folding problem that's not a lookupped thing ?
Regards,
Daniel B Kolis
my ref: af2, 24 Jan 2023
boj Ko
Jan 24, 2023, 1:55:24 PM1/24/23
to diy...@googlegroups.com
I have heard that Some of these include genetic algorithms, Monte Carlo simulations, and simulated annealing. All of these methods involve generating and testing different solutions in order to find the optimal solution to a given folding problem.
вт, 24 янв. 2023 г. в 19:59, Dan Kolis <dank...@gmail.com>:
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Dan Kolis
Jan 25, 2023, 11:55:38 AM1/25/23
to DIYbio
Maybe my question was insufficiently constructed. I suppose it has two parts.
1) Is there a submit any protein coded span and get a folded thing back facility for AF2 anywhere on a public or 'sort-of' public Server ?
2) Is my expectation for such a thing in a R&D group out of order, somehow ? That is when they boast the have AF2 running locally anyway.
I cant see the point in having a simply duplication of PDB except the o/p is machine intelligence. Some submit / return thats structured info better then email might be desirable too. Well, the notion of watching it 'go' is sort of exciting really I suppose.
Regards,
Daniel B Kolis
1) Is there a submit any protein coded span and get a folded thing back facility for AF2 anywhere on a public or 'sort-of' public Server ?
2) Is my expectation for such a thing in a R&D group out of order, somehow ? That is when they boast the have AF2 running locally anyway.
I cant see the point in having a simply duplication of PDB except the o/p is machine intelligence. Some submit / return thats structured info better then email might be desirable too. Well, the notion of watching it 'go' is sort of exciting really I suppose.
Regards,
Daniel B Kolis
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