iiinova — where your digital self keeps evolving

Charlie Harris @harrisbio.bsky.social · 14/04/2025

Small personal update: very pleased to be in Singapore next week to present 2 spotlight papers at ICLR 2025 on AI for molecular design!! 🇸🇬 DM me if you want to meet up and chat about AI for bio, drug discovery, science policy or just chat about aviation!!!

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Charlie Harris @harrisbio.bsky.social · 23/01/2025

I’m very biased but great list of ML for Drug Discovery and resources and blogs by @wpwalters.bsky.social !

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Charlie Harris @harrisbio.bsky.social · 13/01/2025

1/ Just read through the Matt Clifford AI Action Plan now. Tl;dr: it's great but here are a few things that stood out to me as someone interested in AI for Science and sovereign compute and data capability. A thread: 🧵

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Austin Tripp @austinjtripp.bsky.social · 10/01/2025

A common issue I see in ML, both from ML "experts" and "users", is overly optimistic assumptions. "experts" (people designing algs) usually assume the data is very simple "users" (people using algs) usually assume that algorithms are more robust than they really are Conclusion: always be careful!

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Charlie Harris @harrisbio.bsky.social · 11/01/2025

Added NewCo Kerna Labs, a new AI-first mRNA payload design company founded by former Moderna CSO with $6M in seed. Also added new Cradle Bio series B worth $73M

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Charlie Harris @harrisbio.bsky.social · 09/01/2025

Just added Graph Therapeutics, a new startup in Vienna focusing on precision medicine for inflammation and immunology Founded by former Allcyte team

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 13/12/2024

📣 Save the dates 📅 We are organizing a Benzon Symposium on "Protein structure prediction and design" with what I think is an amazing set of speakers Meeting will take place in Copenhagen 🇩🇰 on Sept. 1–4, 2025, and abstract submission will open in March (benzon-foundation.dk/benzon-sympo...)

Flyer for a Benzon Symposium on Protein structure prediction and design in biology and pharmacology (Sept. 1–4, 2025). Speakers include: Gabriel Rocklin, Birte Höcker, Amy Keating, Tanja Kortemme, Bruno Correia, Sarel Fleishman, Ashutosh Chilkoti, Minkyung Baek, Noelia Ferruz, James Fraser, Alan Moses, Susan Marqusee, Ben Lehner, Mohammed AlQuraishi, Dek Woolfson, Gustav Oberdorfer, Hannah Wayment-Steele, Ora Schueler-Furman, Jenifer Listgarten, Alexander Rives, & Max Bonomi.

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Charlie Harris @harrisbio.bsky.social · 10/12/2024

Extremely pleased to announce that after *checks notes* 2 years, our paper on Structure-based Drug Design with diffusion models has been published in Nature Computational Science (@natcomputsci.bsky.social)!! Thanks a lot to the great co-authors! Esp @rne.bsky.social & Yuanqi Du.

nature.com

Structure-based drug design with equivariant diffusion models - Nature Computational Science

This work applies diffusion models to conditional molecule generation and shows how they can be used to tackle various structure-based drug design problems

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Charlie Harris @harrisbio.bsky.social · 04/12/2024

How to come SOTA on protein-ligand binding…. Use Vina (and nothing better) on a single starting conformer Works every time;)

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Charlie Harris @harrisbio.bsky.social · 04/12/2024

🚨I have updated the TechBio Company Database with a bunch of new companies! Find it here: tinyurl.com/techbiodatabase New ones are: - Enveda Biosciences (Natural Products) - Cure_51 (Personalised Medicine) - Antiverse (Antibodies) - Tamarind Bio (SaaS) - Biorelate (Target ID) cont.

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Arne Elofsson @handle.invalid · 03/12/2024

AF3 BEST METHOD followed by cluspro but also some conversion errors

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Charlie Harris @harrisbio.bsky.social · 03/12/2024

In other words, we are still really bad at structure prediction UNLESS we have very rich sequence information from which to infer spatial contacts (?) Same applies to ligand binding obviously

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Charlie Harris @harrisbio.bsky.social · 03/12/2024

Was very fortunate to be invited to give a talk on AI for Drug Discovery at the (very nice) British Ambassador's Residence in Rome last week! Thanks to the Foreign Office for the invitation!

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Philippe Schwaller @pschwllr.bsky.social · 02/12/2024

We are hiring (resharing appreciated)! Given recent successful grant applications (I got my SNSF Starting Grant 🚀), we are extending the LIAC team with multiple openings (PhD/postdoc) for 2025. Apply now (deadline: December 20th) by filling in this form: forms.fillout.com/t/eq5ADAw3kkus. #ChemSky

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Brady Johnston @bradyajohnston.bsky.social · 02/12/2024

More material tests, this time extra squishy. MD trajectory that shows an aspirin ligand coming out of hibernation for spring (undbinding) #b3d #MolecularNodes #GeometryNodes #SciArt

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Charlie Harris @harrisbio.bsky.social · 02/12/2024

Actually a bit sad that I have never, and probably will never, attend CASP:( (unless I get a lot of spare time and funding) So important for driving the revolution in AI for structural biology that’s still taking place right now!

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Torsten Schwede @torstenschwede.bsky.social · 02/12/2024

Assessors’ conclusions of the 3D category (individual protein chains) of #CASP16 🧪

Conclusions of assessment of 3D category

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Charlie Harris @harrisbio.bsky.social · 21/11/2024

Now I can share external links without the posts being down regulated - I thought it would share this again!:) I have compiled a list of now 100+ companies in the 'TechBio' space into a fully open database for the community. Find here and please share if you like open.substack.com/pub/harrisbi...

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Chaitanya K. Joshi @chaitjo.bsky.social · 21/11/2024

Random thought: Did the DL x proteins academic research community sort of move on from antibody design to enzyme design? Everyone following the trend? Some of the discourse around antibodies may make it seem like de novo design given any target is ‘solved’, but this is not true as far as I know…

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