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Thomas Coudrat

@tomsilico

Computational chemistry and AI for drug design in biotech #compchem | CSIRO, Melbourne AU

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03.10.2023
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Latest posts by Thomas Coudrat @tomsilico

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Registrations and abstract submission for the 23rd Melbourne Proteins Group Student Symposium are still open!
16th July, Bio21 Institute, Melbourne.

Register here!
www.eventbrite.com.au/e/mpg-23rd-s...

05.06.2025 01:38 πŸ‘ 0 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0
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Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.

www.biorxiv.org/content/10.1...

06.12.2024 08:38 πŸ‘ 441 πŸ” 147 πŸ’¬ 21 πŸ“Œ 29

Here's a new one with an interesting overlap bsky.app/profile/yiec...

23.11.2024 02:40 πŸ‘ 7 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

#compchem

23.11.2024 02:39 πŸ‘ 11 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

#compchem

22.11.2024 14:09 πŸ‘ 5 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

#compchem

20.11.2024 19:50 πŸ‘ 2 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0

You might find some of these of interest, cheers bsky.app/profile/ckel...

20.11.2024 12:06 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

#compchem

20.11.2024 11:26 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

#compchem

20.11.2024 11:24 πŸ‘ 4 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

#compchem

20.11.2024 07:36 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

#compchem

19.11.2024 20:52 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
Medicinal Chemistry - WCAIR How does a drug come to be a drug?Β  Drug design encompasses organic synthetic chemistry, pharmacology and biology and falls under the name β€œMedicinal Chemistry”.Β  Medicinal chemists are engineers of t...

As for the #medchem and #drugdiscovery training resources (freely available) we have recorded talks on Medicinal Chemistry-related topics: physicochemical properties, metrics in drug design, PAINS, and hERG blockers:

wcair.dundee.ac.uk/training/tra...

#ChemSky

19.11.2024 10:05 πŸ‘ 1 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0

#compchem

19.11.2024 08:33 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
Andrea Andrews-Morger: Federated learning in computational toxicology
Andrea Andrews-Morger: Federated learning in computational toxicology YouTube video by RDKit

Also note this alternative federated learning approach talk at the RDKit UGM: www.youtube.com/watch?v=Y1mj...
paper: pubs.acs.org/doi/10.1021/...

19.11.2024 01:51 πŸ‘ 2 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0
Novatis' public surrogate datasets

Novatis' public surrogate datasets

Interesting thread! I'll add Novartis' recent approach of releasing "surrogate datasets", which are publicly available molecules for which they ran their internal model's predictions: 16K on 4 CYP inhibition assays, 274K on 25 ADME end points. See this talk: youtu.be/LPYk1Jy2E1c?...

19.11.2024 01:48 πŸ‘ 1 πŸ” 1 πŸ’¬ 1 πŸ“Œ 0

#compchem

18.11.2024 19:45 πŸ‘ 3 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

#compchem

18.11.2024 19:41 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Thank you! And yes I'm following Andreas' YouTube channel, cheers

18.11.2024 15:44 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

I'm surprised I didn't know about this before, seems like a great series. Are seminars recorded by any chance? And thanks for posting cheminformatics course content too, I might use this for future students!

18.11.2024 15:22 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

#compchem

18.11.2024 15:13 πŸ‘ 1 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0

#compchem

18.11.2024 15:12 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Could you please add me? Thanks for starting this one!

18.11.2024 15:01 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
About Mol*

Suite of tools for 3D molecular data on the web
Custom WebGL rendering engine
Scales from single atoms to cells with billions

Wanted nicer lighting that still scales
β€œPath-traced” SSGI
Screen-space, so OK with billions of atoms
Sample-based, so good to adjust quality

About Mol* Suite of tools for 3D molecular data on the web Custom WebGL rendering engine Scales from single atoms to cells with billions Wanted nicer lighting that still scales β€œPath-traced” SSGI Screen-space, so OK with billions of atoms Sample-based, so good to adjust quality

Gave a short presentation on Illuminating Molecules in #molstar at the November 2024 #WebGL & #WebGPU Meetup

www.khronos.org/events/webgl...

17.11.2024 21:47 πŸ‘ 14 πŸ” 5 πŸ’¬ 1 πŸ“Œ 0
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Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

17.11.2024 16:20 πŸ‘ 609 πŸ” 204 πŸ’¬ 18 πŸ“Œ 25

You could add @farzanejp.bsky.social too

17.11.2024 17:47 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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Comparative evaluation of methods for the prediction of protein–ligand binding sites - Journal of Cheminformatics The accurate identification of protein–ligand binding sites is of critical importance in understanding and modulating protein function. Accordingly, ligand binding site prediction has remained a resea...

Very interesting benchmark of 13 state-of-the-art protein-ligand binding site prediction, including geometry-based, energy-based and #machinelearning methods.

jcheminf.biomedcentral.com/articles/10....

#chemsky #compchem

17.11.2024 08:39 πŸ‘ 13 πŸ” 2 πŸ’¬ 1 πŸ“Œ 0

#compchem

17.11.2024 17:32 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Save the date: I'm happy to announce that the 2025 RDKit UGM will take place in Prague, Czechia from 10-12 September.
The organizers are Martin Ε Γ­cho and Daniel Svozil from the University of Chemistry and Technology in Prague.

Registration details will follow early next year.

22.10.2024 07:31 πŸ‘ 50 πŸ” 22 πŸ’¬ 0 πŸ“Œ 3
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Postdoc in Protein Computational Biology / Structural Bioinformatics - VIB Job description We are seeking a postdoc to join the Pereira Lab for an interdisciplinary project that integrates structural bioinformatics, protein evolution, complex network analysis, and deep learn...

🚨The future Pereira lab is hiring!

We will start at @vibai.bsky.social in Feb 2025 and are looking for a postdoc to join our team πŸ€“

If you want to leverage AI and large networks to explore and understand the protein universe 🌌, check below!

*deadline: 21 Nov 2024*

jobs.vib.be/j/93314/post...

16.11.2024 21:07 πŸ‘ 24 πŸ” 13 πŸ’¬ 1 πŸ“Œ 1

Interested in the open source software ecosystem for drug discovery? Give the Open Molecular Software Foundation (@omsf.bsky.social) a follow!

16.11.2024 01:31 πŸ‘ 18 πŸ” 5 πŸ’¬ 1 πŸ“Œ 0