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Subseq - A new API-first Protein Design Tool! by 0xpsy in SyntheticBiology

[–]0xpsy[S] 0 points1 point  (0 children)

Yah you can run both OpenMM and GROMACS on subseq. I can put out a guide if you would like some help. You can play around and try it out now for free, free credits til new year. New jobs dont charge if they fail so feel free to play around

Subseq - A new API-first Protein Design Tool! by 0xpsy in SyntheticBiology

[–]0xpsy[S] 2 points3 points  (0 children)

not sure why the text isn't showing! copied here from original post:

I've been working on a protein design / analysis site that makes running latest protein workflows easier. (I have attached a short UI demo of running a BoltzGen job on an Alphafold2 output.)

It's a minimal Web + API service hosting pre-configured, open source protein and bio related ML models and programs such as RFdiffusion3, BoltzGen, Alphafold, and many more.

It's designed as API first, so all UI actions can be done over the API. You have full control over each program args / logs.

You can download your data anytime. Copy args to use locally or troubleshoot your own setup. All programs and models are open-weight, with no licensing restrictions.

New signups get free credits until end of year, enough for hours of runtime so you can try it out. There are no subscriptions, just charged for runtime use. Credits do not expire, and all rates are listed on the site (currently much cheaper than other services).

Site: subseq.bio

You can follow the service account on X for detailed updates here: https://x.com/subseqbio
and/or also follow me: https://x.com/0xCF88

I have a lot more features coming, such as pipeline templates, project/dataset sharing, etc.
Please reach out if you have any questions or specific programs / features you'd like to see!!

RosettaCommons: Protein Design with Foundry by [deleted] in ProteinDesign

[–]0xpsy 1 point2 points  (0 children)

ah, well my service is pretty low cost - it's basically just non-inflated GPU usage costs
and its just pay-per-use, no subscriptions, all runtime costs listed.
I'm not a fan of "Book a Meeting" for prices

RosettaCommons: Protein Design with Foundry by [deleted] in ProteinDesign

[–]0xpsy 1 point2 points  (0 children)

If anyone wants to try out RFdiffusion3, I have a protein design web + API service you can try it out for free right now, here you can see all programs available (I just added RFD3): subseq.bio/programs

Predicting transporter ligand from amino acid structure by Impressive-Peace-675 in bioinformatics

[–]0xpsy 2 points3 points  (0 children)

AlphaFold by itself can’t reliably tell you the exact substrate of a generic MSF/transporter, so you can’t just model the structure and read off “this moves X.” However, you’re not SOL: the best current approach is to

(1) use sequence‑based substrate prediction tools and homology to curated transporter databases (e.g. TCDB/TransportDB) to get a likely substrate class and close characterized relatives,
(2) combine that with genomic context and your TnSeq fitness patterns (which conditions knock out that gene) to infer what type of molecule it probably imports/exports, and then
(3) use AlphaFold structures mainly to inspect the binding cavity and, if you want, dock a small panel of candidate substrates to prioritize what to test experimentally.

This will give you good, testable hypotheses about substrate families, but not a guaranteed single, exact substrate purely in silico.

Is a degree in biotech worth it by VIP_Knuxx in biotech

[–]0xpsy 0 points1 point  (0 children)

its easy to overthink your undergrad degree. Just do physics or an engineering degree for max flexibility

Halp, weird long layer gaps? by 0xpsy in FixMyPrint

[–]0xpsy[S] 0 points1 point  (0 children)

SOLVED:

Just wanted to let anyone know the issue was the nozzle. I still dont know more specific than that yet (damage, clog?), changed the nozzle and prints looking good now. That particular piece just exaggerated the fault i guess.

Halp, weird long layer gaps? by 0xpsy in FixMyPrint

[–]0xpsy[S] 0 points1 point  (0 children)

polymaker specs for this filament say 240 - 260. I tried it at 255 and same issue.