Chris Ing

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Chris Ing

Chris Ing

@jsci

Co-Founder, CSO at @proteinqure, @UofT @UWaterloo. Peptide Therapeutics, Structure-based Drug Design, Computational Biophysics, AI for Drug Discovery, Cats

Toronto, Ontario Katılım Mayıs 2009
1.7K Takip Edilen1.3K Takipçiler
Chris Ing
Chris Ing@jsci·
@MartinPacesa @DdelAlamo Professional antibody designers will tell you can't have any fun when it comes to the surface; their genius insights are like: sorry sir you can't have positive, negative, hydrophobic, or any patches of any kind, or else you won't have a chance in hell of being clinical stage😮‍💨
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Martin Pacesa
Martin Pacesa@MartinPacesa·
@DdelAlamo Glutamate's are goooooood Diego, I personally would throw in some more :D they keep proteins from sticking together and to nucleic acids
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Diego del Alamo
Diego del Alamo@DdelAlamo·
In my experience, if you train from-scratch MPNN (or probably any inverse folding model), early epochs show disproportionate # of leu, lys, & glu (gly and pro also get added early due to unique phi/psi). This goes away as you keep training; MPNN might not have been trained enough
Clay Kosonocky@kosonocky

Then, we find that these alpha helices are extremely enriched in lysine and glutamate, with over 35% of the residues in the design being contained in an K+E alpha helix. This feature alone obtains 0.89 ROC-AUC when used to train a LR to predict recovery across all 12000 sequences

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Chris Ing
Chris Ing@jsci·
@DdelAlamo "How should we adjust the design of our drug candidate to account for octopus physiology?"
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Chris Ing
Chris Ing@jsci·
@sid_srk I acquired my refined taste through the grind
Chris Ing tweet media
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Sid
Sid@sid_srk·
Everyone talks about *having* taste, but no one talks about how to acquire it. There are no shortcuts, don’t fool yourself into thinking this is a great equalizer, the process is where the magic is.
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Diego del Alamo
Diego del Alamo@DdelAlamo·
Does anyone know if the Boltz team has made any effort to get their papers peer-reviewed and published “officially”? Because if not, I have tons of respect for them for choosing not to play that game
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OpenAI
OpenAI@OpenAI·
We worked with @Ginkgo to connect GPT-5 to an autonomous lab, so it could propose experiments, run them at scale, learn from the results, and decide what to try next. That closed loop brought protein production cost down by 40%.
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Chris Ing
Chris Ing@jsci·
@LeoCK_Wan hard mode: de novo ribosome, orthogonal translation engine that natively reads quadruplet codons, incorporates wild non-canonical monomers, and macrocyclizes on exit to print drug-like peptides on demand. Speed/fidelity/yield optimization a bonus ;)
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Leo Wan
Leo Wan@LeoCK_Wan·
You have lab in the loop capabilies. Protein design, high-throughput screening, validation. What protein would you make or evolve?? Enough good ideas and we might actually do it
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Chris Ing
Chris Ing@jsci·
Expired: "One-click binder design" Tired: "One-sentence binder design" Wired: "One-epic-saga binder design"
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Chris Ing
Chris Ing@jsci·
I'm not seeing much work done on human dispatch APIs. My agent seems suspiciously excited to make a programmatic TaskRabbit it can use to vicariously "touch grass"...
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Chris Ing
Chris Ing@jsci·
@Ronalfa @owl_posting Hmm, but if the barrier to create a whole LLM competitive intelligence platform is so low, how competitive is it?🤔
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Ron Alfa
Ron Alfa@Ronalfa·
FMs aside, @owl_posting in his free time built a whole LLM competitive intelligence platform to feed our clinical analysis pipeline. You can just do things.
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Chris Ing
Chris Ing@jsci·
Democratising real-world drug discovery through agentic AI (doi.org/10.1016/j.drud…). Putting these agents through the wringer with tasks like "What is the SMILES string of ibuprofen?"😇
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Chris Ing
Chris Ing@jsci·
@aaronmring @MartinPacesa Experimental screening doesn't seem to have helped much. Success rates for LatentX + Flash Display (2/6), BindCraft + Flash (0/4) vs. LatentX Alone (0/5), BindCraft Alone (2/100)
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Aaron Ring
Aaron Ring@aaronmring·
@MartinPacesa This is super useful, Martin. One problem is that some of these methods benefitted from experimental pre-screening and so their actual success rates may be significantly inflated. I think in future competitions Adaptyv should ban this. Congrats on a great BC2 result!
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Chris Ing
Chris Ing@jsci·
@btnaughton @modal Gotta hand it to these guys (and in silico metrics), many of these ended up being solid binders!
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Brian Naughton
Brian Naughton@btnaughton·
Another excellent protein design blogpost from Nick Boyd and Sam Guns at Escalante. They got the top scoring design (in silico score that is!) in the Adaptyv Bio Nipah competition using a very concise script, running mosaic on @modal so anyone can run it blog.escalante.bio/180-lines-of-c…
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Chris Ing
Chris Ing@jsci·
@sid_srk But models can also enable epistemic agency (journals.aps.org/prper/abstract…). That implies choices that can change the problem itself. If the hypothesis space is operational, goals emerge from constraints, allowing non-canonical paths without narrative steering.
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Sid@sid_srk·
@jsci “Become Schrodinger in 1925” is an exercise in agency from a user’s pov. I also believe better storytelling leads to higher agency. imo “complete this assignment” interpretation of better stoytelling is a bit reductive
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Sid@sid_srk·
This is the most exciting time for new education tools. I'm revisiting physics I learned in high school, which I had little appreciation for at the time, but it's so fascinating now. I think that as AI matures, the future will involve humans deriving joy from understanding all the advances we will see. Not just willing these advances into existence but teaching ourselves new things about the way our universe functions.
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Chris Ing
Chris Ing@jsci·
@sid_srk Scaffolding helps, but the hard problem in theoretical physics is agency, not context. "Become Schrödinger in 1925" still reenacts known paths. Unless AI creates new goals, ways to act and discover, it's just "complete the assignment" with better storytelling.
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Sid
Sid@sid_srk·
if someone found the goals listed by the model here as-is to be motivating, I'd guess that they're already attuned to pursuing theoretical physics or adjacent fields. I think the work lies in laying the narrative foundation for these concrete goals. For instance, instead of saying "derive the Schrödinger equation", the model could say "here's the times Schrödinger lived in, this is what was known about matter at the time, deBroglie recently put forth information about wave like properties of matter, how would you reconcile these different observations made by different physicists and construct an equation that could explain these?" I think that scaffolds matter a lot for learning and building a good system that drives and directs the learner to ask information-maximizing questions is non-trivial. It's not going to come from asking the models "teach me "
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Chris Ing
Chris Ing@jsci·
Boltz Pro Tip: Don't know what your ligand is? Use atom element "X" for ambiguous atom type (ambiguous monomer ASN/ASP depicted rcsb.org/ligand/ASX). Accuracy not guaranteed 😅
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Chris Ing
Chris Ing@jsci·
Facebook Marketplace: "Hello, is this still available?" "Yes. Then you’re interested?" "Only if it’s available." "It is." "Then I will consider it." "We are considering." (They do not move.)
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Chris Ing
Chris Ing@jsci·
Yearly tradition to summarize my faves, 2025: Song: "9 2 5", "Afterlife" Album: "Baby" by Dijon Movies: One Battle After Another, Sinners Series: Chair Company, Severance S2, The Pitt S1 Comics: Drome Game: Clair Obscur, Blue Prince Anime: Chainsaw Man Reze Arc, To Be Hero X
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