4 ms·
> The total download size is around 428 GB and the total size when unzipped is 2.2 TB. Please make sure you have a large enough hard drive space, bandwidth and
by gopalv 5y ago
> The total download size is around 428 GB and the total size when unzipped is 2.2 TB. Please make sure you have a large enough hard drive space, bandwidth and time to download.
> This was tested on Google Cloud with a machine using the nvidia-gpu-cloud-image with 12 vCPUs, 85 GB of RAM, a 100 GB boot disk, the databases on an additional 3 TB disk, and an A100 GPU.
This is amazingly detailed for a researcher who wants to follow in the track and also Apache licensed, which is one road-bump out of the way for a commercial enterprise, like an actual drug manufacturer who wants to burn some money trying this out.
edit: said the last part too fast, the code has a "the AlphaFold parameters are made available for non-commercial use only under the terms of the CC BY-NC 4.0 license"
- dekhn 5y agoYes, all science should be communicated in the form of an academic paper wiht a supporting git repo and quickly downloadable dataset and a fast path to reproducing the work. That would be a huge change from the establishment. It's quite unclear what value this will have to pharma; personally I doubt this has any direct applications (and I'm one of the few people in the world that can say that with deep authority).
- aantix 5y agoWho benefits from this work?
- dekhn 5y agoPrimarily the community that previously depended on homology models.
- deleted 5y ago[deleted]
- gnufx 5y agoSurely not all science. Just as well Dirac wasn't required to communicate that way the equation that fundamentally underlies the phenomenon discussed, and you couldn't put the unique facility my thesis work pioneered into git! I do highly approve of publishing software and data where possible, of course, since before Free Software needed to be coined, and it's much easier now.
- dekhn 5y agoIf you're just publishing equations, you should have an associated notebook which executes the equations. I don't know what you mean you can't put your thesis work into git. Is it a physical thing? Too big for git?
- jhrmnn 5y agoEquations are math. They can be used analytically with pen and paper. No need to turn them into code.
- astro-codes 5y agoWhy wouldn't this have much value to pharma? Is it because its application is actually really limited in scope?
- dekhn 5y agothere are research groups this would be useful for but structures are not on the critical path to drug discovery or approval.
- exikyut 5y agoOut of (probably overoptimistic :) ) curiosity, what do you see are the critical paths?
- l33tman 5y agoI've been doing protein pharma research and the structure is only a first step, then years of figuring out the kinematics and dynamics of the protein, figuring out how it works, how all the natural ligands bind and affect the kinematics.. and only after all that you might conceivably start to engineer drug compounds (unless you bootstrap by a natural ligand to tweak "randomly", but then again, that's how pharma development traditionally works). Still, even if structure determination is not on the "critical path", it IS a big barrier that has (started) to fall now.
- dekhn 5y agoInitial molecule generation and FDA approval.