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!!!

Huge thanks all experts who have contributed w/ input and feedback! @rory.bio @areeq.bsky.social @leecronin.bsky.social @erika-alden.bsky.social @econormist.bsky.social @saakohl.bsky.social @mariokrenn.bsky.social @stianwestlake.bsky.social @harrisbio.bsky.social @richardaljones.bsky.social 11/11

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

Pat Walters@wpwalters.bsky.social · 2y ago

Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...

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: 🧵

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!

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

Charlie Harris@harrisbio.bsky.social · 2y ago

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...

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

Charlie Harris@harrisbio.bsky.social · 2y ago

🚨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.

📣 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...)

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.

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

nature.com

Now added Aqemia as well

Aqemia - Discovering Drugs with Deep Physics and AI

Aqemia is an in silico drug discovery start-up, whose ambition is to discover rapidly more innovative therapeutic molecules with better chances of success.

aqemia.com

Charlie Harris@harrisbio.bsky.social · 2y ago

🚨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.

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

Peter Koo@pkoo562.bsky.social · 2y ago

🚨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.

AF3 BEST METHOD followed by cluspro but also some conversion errors

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

Torsten Schwede@torstenschwede.bsky.social · 2y ago

Conclusion of RNA assessors in #CASP16 - we are still in the “template” phase. Prediction of nucleic acids structure is still challenging for targets without templates, often relying on intuition. No big leap in accuracy since CASP15. AI based methods have not (yet?) made a major difference.

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!

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

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

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!

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

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...

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…