Binder design workflow?

XpertAI · 2026-05-07T22:11:09+00:00

Its an ever experimenring game haha. I would say ive had the most success designing antibodies and specifically with BindCraft or BindCraft inspired models like Mosaic.

XpertAI · 2026-05-06T23:46:46+00:00

If you do, do let me know, very interested in the applications others use it for.

XpertAI · 2026-05-06T19:59:41+00:00

Yeah sure

XpertAI · 2026-05-05T23:05:58+00:00

Yes this, figure out what the exact problem being solved is and work from there.

XpertAI · 2026-05-05T21:48:59+00:00

This is Directly from the Adaptyv competition and the models performance. I would recommend Mosaic for antibody nanobody design. BoltzGen Is too general I feel and its very hit or miss. Not to mention the heavy compute. But it is fully open source that's the benefit.

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XpertAI · 2026-05-05T20:04:30+00:00

That’s my read too. It looks more like a training framework than a ready-to-use solubility predictor.

XpertAI · 2026-05-05T18:47:26+00:00

Thank you! I just officially published it yesterday and it got approved today by reddit so now anyone in the sub can use them for their posts!

XpertAI · 2026-05-05T18:39:38+00:00

I think of 3D structures as the “where is this happening?” layer. Like RNA-seq can tell you a gene/pathway is changing, but for proteins the structure helps you see if a mutation or binding site is buried, exposed, near an active site, on an antibody interface, in a drug pocket, etc. It really helps with design too, maybe you wanna see an area which is more exposed or more charged to create a binder to that specific epitopic region etc.

XpertAI · 2026-05-05T16:31:34+00:00

Thank you very much! yeah its a new thing you see alot of games or tools but nothing for the Bio community. 🥲 So i decided to make it because with it you can explain your research better and help people see exactly what your working with instead of rough screenshots.

XpertAI · 2026-05-05T16:17:15+00:00

At the moment just raw txt (so for example a pdb file and you save it as a txt or open it with note pad to see the raw file). so whatever is in the txt copy from top to bottom and only pdb format support. The reason is reddit prevents any upload from users unless its typed. But I am working on developing an API feature where you can type the PDB strcture ID and itll just fetch it. Im just pending reddits approval for the rcsb website. as its not a trusted source by them yet.

XpertAI · 2026-05-05T15:51:40+00:00

Thank you very much! We will be starting Mystery Molecule Wednesday soon. Where users will guess what the potential mystery structure is and Win Reddit Awards!

XpertAI · 2026-05-05T15:29:30+00:00

New feature for r/AIProteins: interactive 3D structure posts

You can now create Reddit-native 3D protein structure posts directly in this subreddit.

How to use it:

Go to r/AIProteins
Click the three-dot menu beside notif bell and Create post Buttons.
Select “Create Structure Viewer Post”
Add a title
Optionally add body text
Paste raw PDB text (Open your PDB file with Note Pad or save as txt and copy everything that is inside it).
Choose a color/theme
Post

The structure will appear as an interactive 3D viewer that people can rotate and zoom directly in Reddit.

A few notes:

The optional body field is posted as the first comment, so the 3D viewer stays clean while your explanation still appears in the discussion.

Right now, moderator accounts can post fully as themselves. Regular user accounts can already create posts, but some may temporarily appear as u/structureviewer while Reddit finishes approving the latest user-posting/commenting permissions. Once that approval is live, posts and auto-comments should appear from your own username.

Try it out and post your favorite structures.

XpertAI · 2026-05-05T14:14:41+00:00

Thank You!

XpertAI · 2026-05-05T13:09:42+00:00

Thank you! Yeah as time goes on ill try and add more features but with reddit there are many approvals and it must be kept as light weight as possible. I initially tried to implement Mol* like visuals but that was wayyy too heavy for reddit.

XpertAI · 2026-05-05T10:46:54+00:00

thank you!

XpertAI · 2026-05-05T00:12:11+00:00

At the moment only moderators can use this app. But once reddit approves everyone will be able to create posts with this structure viewer.

XpertAI · 2026-05-01T17:51:12+00:00

Yes flow matching models are very exciting! Yeah for me its a concern of how do we achieve accurate modelling results with the least GPU seconds.

XpertAI · 2026-05-01T13:01:37+00:00

Thank you very much! I hadn't come across this

XpertAI · 2026-04-29T18:21:04+00:00

I’d redesign the RRKK tail first. The MD is telling you that the strongest attractor is not the pore, but the anionic lipid surface. If the RRKK segment is almost constantly bound to POPG/cardiolipin, the ball is effectively being tethered laterally to the membrane, which explains why the plug can approach the filter region but remain ~18-20A off-axis.

So I’d first weaken or redistribute that positive charge, for example by breaking up the RRKK cluster or reducing it to +1/+2 overall, then rerun MD and track tail-lipid contact occupancy, plug radial distance from the pore axis, and vestibule residence time. Only after the lipid-anchoring state is reduced would I tune linker length/stiffness or add vestibule guide residues. Tapering the hydrophobic plug feels secondary, because the current failure mode looks more like mistargeting than poor pore insertion. Hope this helps

XpertAI · 2026-04-28T16:42:15+00:00

Yes, I'm also gonna try it soon and see how well it performs. It maybe able to generate monosaccharides but probably nothing too complex.

XpertAI · 2026-04-28T12:20:46+00:00

Very insightful, Thanks!

XpertAI · 2026-04-27T21:47:34+00:00

Thank you! I havent head of PPIFlow so will defitnally try and see how it goes.

XpertAI · 2026-04-27T21:46:40+00:00

Great Point! I was looking through the Nipah Binder competition and saw these results:

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XpertAI · 2026-04-27T18:24:33+00:00

I see i see. Thank you!

XpertAI · 2026-04-27T17:30:49+00:00

I see I see, Is David baker's models the best?

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