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Back to 🔬 Lab-in-the-Loop at Compute Speed — Ian Quigley, Leash Bio, with Ian Quigley & RJ Honicky.

How Reproducible Are Leash Bio Binding Screens?

Ian Quigley says about 90% of chemicals that are easy in their hands still work after they are made off DNA and run in functional assays, and about 50% of the hard ones do.

For machine learning, the chemicals stay in the tube with DNA barcodes. Some bind and some do not, and the binding is signal measured from the world. Models are conditioned on the barcode, with a placeholder that marks where the DNA sits. Leash does not pretend the DNA is missing. Fresh protein batches and a new chemical library, rerun over many months, bring back the same hits in the same order for the most part. The screen is extremely reproducible and robust. Making the molecule without the DNA for a drug is where the attrition shows up. The molecule has to be made again, and sometimes it behaves differently. Not always, but sometimes.

Because the barcoded result repeats, he treats it as solid ground-truth signal and keeps training.

Transcript

🔬 Lab-in-the-Loop at Compute Speed — Ian Quigley, Leash Bio ·

Latent Space: The AI Engineer Podcast

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  1. Who Hosts Latent Space AI for Science?RJ Honicky hosts Latent Space AI for Science with Brandon Anderson.
  2. How Many Molecules Can One DNA-encoded Library Hold?Ian Quigley says the largest DNA-encoded library produced holds 40 trillion molecules, while the biggest one-chemical-at-a-time collections sit in the low…
  3. Which Lab Measurements Can Actually Scale?Ian Quigley says that if life science is going to be paired with machine learning, the only scalable readout is taking pictures, and sequencing DNA is another…
  4. How Does Leash Bio Find Binding Chemicals?Ian Quigley says Leash Bio finds binding chemicals by fixing a protein target on a magnetic bead, dunking the bead in a barcoded mixture, and sequencing the…
  5. What Is a Small Molecule Drug?Ian Quigley calls a small molecule a tiny chemical that can sit in a pill, go inside a cell, and affect how a protein behaves.
  6. Did Anyone Beat Chance on the Hardest Leash Bio Binding Test?Ian Quigley says that on the hardest split of Leash Bio's public binding contest, nobody did better than chance, and three of the top five entries were a…
  7. Why Do Binding Models Learn the Chemist Instead of the Chemistry?Ian Quigley says a model can predict ChEMBL activity from who probably made a molecule about as well as it can from the chemical formula, so it is learning…
  8. Did Hermes Match Boltz on Binding Prediction?Ian Quigley says Hermes did about as well as Boltz, then the state of the art structural model, on public data sets for binding prediction.
  9. What Is a Magic Methyl in Drug Design?Ian Quigley says a magic methyl is the medicinal-chemistry story that one tiny thorn on a molecule can make it work or make it fail, and he calls that story…
  10. Why Do Structure Models Put a Drug Back Into a Filled Pocket?Ian Quigley says current co-folding models still place a small molecule where a pocket used to be after that pocket has been filled in, removed, or broken.
  11. How Does Breaking a Protein Pocket Prove Binding?Ian Quigley says breaking one pocket with a mutation shows which chemicals were binding there.
  12. Why Does the Hermes Binding Model Nickname a Protein?Ian Quigley says the Hermes binding model nicknames a protein by memorizing a short variable stretch of amino acids, instead of looking at the binding pocket…
  13. How Does Leash Bio Run Lab-in-the-loop Without a New Experiment?Ian Quigley says Leash Bio runs lab-in-the-loop at compute speed by letting a language model test a binding idea against measurements the lab already…
  14. Why Does a Chemical Library Favor Some Proteins?Ian Quigley says chemical library design depends on the building blocks, a whole library made in one geometry might be really good for some types of protein…
  15. How Many Proteins Has Leash Bio Screened?Ian Quigley says Leash Bio has developed and screened about 2,000 different protein constructs and about 5,000 screens in the history of the company, each…
  16. Why Does Copying Leash Bio Still Take Time?Ian Quigley says a better funded lab still needs time to outscale Leash, because the advantage is a long trail of laboratory mistakes, metadata discipline…
  17. What Small-molecule Cleanup Does Ian Quigley Want?Ian Quigley wants small-molecule cleanup that can run at massive scale. The gizmos that purify well, including HPLC, are not highly parallel.

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