Charlie Harris
@harrisbio.bsky.social
PhD @ Cambridge in AI for Bio | Interested in generative modelling for drug discovery and science policy 🇬🇧
Website: cch1999.github.io
Blog: harrisbio.substack.com
Database: harrisbio.notion.site
Website: cch1999.github.io
Blog: harrisbio.substack.com
Database: harrisbio.notion.site
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!!!
DM me if you want to meet up and chat about AI for bio, drug discovery, science policy or just chat about aviation!!!
April 14, 2025 at 10:19 AM
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!!!
DM me if you want to meet up and chat about AI for bio, drug discovery, science policy or just chat about aviation!!!
Reposted by Charlie Harris
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
@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
February 21, 2025 at 11:42 AM
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
@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 !
Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...
GitHub - PatWalters/resources_2025: Machine Learning in Drug Discovery Resources 2024
Machine Learning in Drug Discovery Resources 2024. Contribute to PatWalters/resources_2025 development by creating an account on GitHub.
github.com
January 23, 2025 at 3:06 PM
I’m very biased but great list of ML for Drug Discovery and resources and blogs by @wpwalters.bsky.social !
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: 🧵
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: 🧵
January 13, 2025 at 7:17 PM
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: 🧵
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: 🧵
Reposted by Charlie Harris
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!
"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!
January 10, 2025 at 9:46 AM
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!
"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
Also added new Cradle Bio series B worth $73M
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...
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...
January 11, 2025 at 4:35 PM
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
Also added new Cradle Bio series B worth $73M
Just added Graph Therapeutics, a new startup in Vienna focusing on precision medicine for inflammation and immunology
Founded by former Allcyte team
Founded by former Allcyte team
January 9, 2025 at 9:37 AM
Just added Graph Therapeutics, a new startup in Vienna focusing on precision medicine for inflammation and immunology
Founded by former Allcyte team
Founded by former Allcyte team
Reposted by Charlie Harris
📣 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...)
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...)
December 13, 2024 at 2:50 PM
📣 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...)
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.
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
www.nature.com
December 10, 2024 at 3:10 PM
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.
Thanks a lot to the great co-authors! Esp
@rne.bsky.social & Yuanqi Du.
Now added Aqemia as well
December 9, 2024 at 11:17 AM
Now added Aqemia as well
How to come SOTA on protein-ligand binding….
Use Vina (and nothing better) on a single starting conformer
Works every time;)
Use Vina (and nothing better) on a single starting conformer
Works every time;)
December 4, 2024 at 2:49 PM
How to come SOTA on protein-ligand binding….
Use Vina (and nothing better) on a single starting conformer
Works every time;)
Use Vina (and nothing better) on a single starting conformer
Works every time;)
🚨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.
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.
December 4, 2024 at 11:31 AM
🚨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.
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.
Reposted by Charlie Harris
AF3 BEST METHOD followed by cluspro but also some conversion errors
December 3, 2024 at 5:07 PM
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
Same applies to ligand binding obviously
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.
December 3, 2024 at 2:06 PM
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
Same applies to ligand binding obviously
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!
Thanks to the Foreign Office for the invitation!
December 3, 2024 at 12:08 PM
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!
Thanks to the Foreign Office for the invitation!
Reposted by Charlie Harris
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
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
December 2, 2024 at 10:33 AM
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
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
Reposted by Charlie Harris
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
December 2, 2024 at 9:25 AM
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!
(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!
December 2, 2024 at 4:39 PM
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!
(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!
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...
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...
November 21, 2024 at 8:53 AM
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...
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...
Reposted by Charlie Harris
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…
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…
November 21, 2024 at 4:01 AM
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…
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…