Matthieu da Costa
@mdc-biocat.bsky.social
Computational Biology - Enzyme Design & Discovery - Chemoinformatics
Abolis Biotechnologies
Abolis Biotechnologies
Mercredi prochain je serai de retour à Villejuif pour les 10 ans d’iGEM IONIS.
Table ronde sur la biologie de synthèse face aux enjeux climatiques que je partagerai avec Andrew Tolonen… mon prof en 2015 et advisor IGEM en 2014.
Table ronde sur la biologie de synthèse face aux enjeux climatiques que je partagerai avec Andrew Tolonen… mon prof en 2015 et advisor IGEM en 2014.
September 18, 2025 at 7:32 PM
Mercredi prochain je serai de retour à Villejuif pour les 10 ans d’iGEM IONIS.
Table ronde sur la biologie de synthèse face aux enjeux climatiques que je partagerai avec Andrew Tolonen… mon prof en 2015 et advisor IGEM en 2014.
Table ronde sur la biologie de synthèse face aux enjeux climatiques que je partagerai avec Andrew Tolonen… mon prof en 2015 et advisor IGEM en 2014.
Reposted by Matthieu da Costa
Excited to announce a preprint describing our software package Meeko! Meeko is a Python package that uses RDKit for receptor and ligand preparation, including protonation, bond order, and connectivity and processing of docking results. It is customizable and suitable for high-throughput workflows.
September 18, 2025 at 12:37 AM
Excited to announce a preprint describing our software package Meeko! Meeko is a Python package that uses RDKit for receptor and ligand preparation, including protonation, bond order, and connectivity and processing of docking results. It is customizable and suitable for high-throughput workflows.
Reposted by Matthieu da Costa
New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...
patwalters.github.io/Three-Papers...
July 22, 2025 at 1:40 PM
New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...
patwalters.github.io/Three-Papers...
With the release of Boltz 2, is there already a review comparing the efficiency of different (new) docking tools? (I’ve already tried Pocket Vina, which is actually quite good for high-throughput)
August 31, 2025 at 12:08 PM
With the release of Boltz 2, is there already a review comparing the efficiency of different (new) docking tools? (I’ve already tried Pocket Vina, which is actually quite good for high-throughput)
Entre deux simulations, épris de rationalité et mu par le désir de progrès, je me plonge dans cet ouvrage qui saura sans doute tempérer mes ardeurs…
August 31, 2025 at 9:41 AM
Entre deux simulations, épris de rationalité et mu par le désir de progrès, je me plonge dans cet ouvrage qui saura sans doute tempérer mes ardeurs…
Reposted by Matthieu da Costa
We have a new preprint out on the Masala software suite, a free and open-source platform for easy biomolecular modelling methods development. www.biorxiv.org/content/10.1...
The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design
Although canonical protein design has benefited from machine learning methods trained on databases of protein sequences and structures, synthetic heteropolymer design still relies heavily on physics-b...
www.biorxiv.org
July 14, 2025 at 1:07 PM
We have a new preprint out on the Masala software suite, a free and open-source platform for easy biomolecular modelling methods development. www.biorxiv.org/content/10.1...
Reposted by Matthieu da Costa
I'm excited to share our new preprint: PocketVina — a fast, scalable, and accurate multi-pocket molecular docking method.
Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating...
Thread - (1/n)
Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating...
Thread - (1/n)
June 26, 2025 at 11:12 AM
I'm excited to share our new preprint: PocketVina — a fast, scalable, and accurate multi-pocket molecular docking method.
Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating...
Thread - (1/n)
Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating...
Thread - (1/n)
Reposted by Matthieu da Costa
🚀 Our paper on the updated PrankWeb, a web app for protein binding site prediction using P2Rank, is out in
@narjournal.bsky.social. Now with docking integration!
👨💻 Try it: prankweb.cz
📄 Paper: doi.org/10.1093/nar/...
💻 GitHub: github.com/cusbg/prankweb
Developed at @cusbg.bsky.social
@narjournal.bsky.social. Now with docking integration!
👨💻 Try it: prankweb.cz
📄 Paper: doi.org/10.1093/nar/...
💻 GitHub: github.com/cusbg/prankweb
Developed at @cusbg.bsky.social
June 10, 2025 at 3:09 PM
🚀 Our paper on the updated PrankWeb, a web app for protein binding site prediction using P2Rank, is out in
@narjournal.bsky.social. Now with docking integration!
👨💻 Try it: prankweb.cz
📄 Paper: doi.org/10.1093/nar/...
💻 GitHub: github.com/cusbg/prankweb
Developed at @cusbg.bsky.social
@narjournal.bsky.social. Now with docking integration!
👨💻 Try it: prankweb.cz
📄 Paper: doi.org/10.1093/nar/...
💻 GitHub: github.com/cusbg/prankweb
Developed at @cusbg.bsky.social
The heptagonal box model is a specificity and activity model that helps identify the type of reaction an enzyme catalyzes and its substrate, but it is not meant to indicate how well the enzyme performs. Structural features clearly play a critical role in catalysis (dynamics, binding, etc.).
May 24, 2025 at 11:56 AM
The heptagonal box model is a specificity and activity model that helps identify the type of reaction an enzyme catalyzes and its substrate, but it is not meant to indicate how well the enzyme performs. Structural features clearly play a critical role in catalysis (dynamics, binding, etc.).
It actually feels like the opposite here in Paris. I keep seeing more and more people with a book in hand on public transport. Even at Abolis, there's a growing habit of sharing and recommending books.
Reading for pleasure has been linked to better sleep, improved mental health and even a longer life - but we're doing it less and less every year.
Reading for pleasure has plummeted over the past 20 years
People in the US are reading for pleasure less and less, despite it being linked to better sleep, improved mental health and even a longer life
www.newscientist.com
May 6, 2025 at 12:31 PM
It actually feels like the opposite here in Paris. I keep seeing more and more people with a book in hand on public transport. Even at Abolis, there's a growing habit of sharing and recommending books.
Reposted by Matthieu da Costa
Proud to announce a new publication from the lab: EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals
www.nature.com/articles/s41...
www.nature.com/articles/s41...
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals - Nature Communications
Despite having structures for most proteins, we still do not know their function. Here, authors introduce EvoWeaver, a de novo method to identify genes working together using evolutionary information....
www.nature.com
April 28, 2025 at 1:47 PM
Proud to announce a new publication from the lab: EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Matthieu da Costa
Close to recreating it in ChimeraX:
1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20
Room for improvement, needs more desaturation
1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20
Room for improvement, needs more desaturation
April 16, 2025 at 6:31 AM
Close to recreating it in ChimeraX:
1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20
Room for improvement, needs more desaturation
1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20
Room for improvement, needs more desaturation
Reposted by Matthieu da Costa
Introducing CAMEO Structures & Complexes - automated weekly blind benchmarking of structure prediction servers. Now with heteromeric and protein-ligand complexes.
Join us and register your server now!
cameo3d.org
Join us and register your server now!
cameo3d.org
April 28, 2025 at 7:56 AM
Introducing CAMEO Structures & Complexes - automated weekly blind benchmarking of structure prediction servers. Now with heteromeric and protein-ligand complexes.
Join us and register your server now!
cameo3d.org
Join us and register your server now!
cameo3d.org
Reposted by Matthieu da Costa
"De novo prediction of protein structural dynamics"
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
delalamo.xyz
April 27, 2025 at 2:16 PM
"De novo prediction of protein structural dynamics"
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
Reposted by Matthieu da Costa
Boltz-1 update Boltz-1x introduces inference-time steering for much higher physical quality, CUDA kernels for faster, more memory-efficient inference and training.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Boltz-1: Democratizing Biomolecular Interaction Modeling
Understanding biomolecular interactions is fundamental to advancing fields like drug discovery and protein design. In this paper, we introduce Boltz-1, an open-source deep learning model incorporating...
www.biorxiv.org
April 27, 2025 at 6:41 PM
Boltz-1 update Boltz-1x introduces inference-time steering for much higher physical quality, CUDA kernels for faster, more memory-efficient inference and training.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Matthieu da Costa
AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
April 27, 2025 at 12:13 AM
AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
Reposted by Matthieu da Costa
Gene synthesis is often the most expensive part of protein engineering with generative models.
Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50.
@philromero.bsky.social
Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50.
@philromero.bsky.social
March 24, 2025 at 5:24 PM
Gene synthesis is often the most expensive part of protein engineering with generative models.
Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50.
@philromero.bsky.social
Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50.
@philromero.bsky.social
Reposted by Matthieu da Costa
Three BioML starter packs now!
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
Pack 3: go.bsky.app/NAKYUok
DM if you want to be included (or nominate people who should be!)
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
Pack 3: go.bsky.app/NAKYUok
DM if you want to be included (or nominate people who should be!)
December 3, 2024 at 3:27 AM
Three BioML starter packs now!
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
Pack 3: go.bsky.app/NAKYUok
DM if you want to be included (or nominate people who should be!)
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
Pack 3: go.bsky.app/NAKYUok
DM if you want to be included (or nominate people who should be!)
Reposted by Matthieu da Costa
RFDiffusion2: a diffusion model that scaffolds enzyme active sites at the atomic level enables the generation of functional de novo enzymes
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 11, 2025 at 7:54 PM
RFDiffusion2: a diffusion model that scaffolds enzyme active sites at the atomic level enables the generation of functional de novo enzymes
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Matthieu da Costa
Small proteins can be more complex than they look!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
March 26, 2025 at 4:21 PM
Small proteins can be more complex than they look!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
Reposted by Matthieu da Costa
Emergence of fractal geometries in the evolution of a metabolic enzyme
Emergence of fractal geometries in the evolution of a metabolic enzyme
Nature, Published online: 10 April 2024; doi:10.1038/s41586-024-07287-2 Citrate synthase from the cyanobacterium Synechococcus elongatus is shown to self-assemble into Sierpiński triangles, a finding that opens up the possibility that other naturally occurring molecular-scale fractals exist.
www.nature.com
April 10, 2024 at 4:38 PM
Emergence of fractal geometries in the evolution of a metabolic enzyme
Reposted by Matthieu da Costa
For future reference, this is the slide (without the bottom cropped) that should have been posted here. Boltz-1 and AF3 are actually performing similarly on the Chymase and Mpro datasets, and differ only on the Autotaxin dataset for still unknown reasons.
December 9, 2024 at 3:38 PM
For future reference, this is the slide (without the bottom cropped) that should have been posted here. Boltz-1 and AF3 are actually performing similarly on the Chymase and Mpro datasets, and differ only on the Autotaxin dataset for still unknown reasons.
Reposted by Matthieu da Costa
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering
Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...
www.nature.com
February 28, 2025 at 2:45 PM
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Reposted by Matthieu da Costa
We are happy to share that the code and weights of PLACER (formerly known as ChemNet) are now public!
This method allows for rapid evaluation of protein side chain and ligand conformational ensembles, with uses in ligand docking and enzyme evaluation.
github.com/baker-labora...
This method allows for rapid evaluation of protein side chain and ligand conformational ensembles, with uses in ligand docking and enzyme evaluation.
github.com/baker-labora...
GitHub - baker-laboratory/PLACER: PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.
PLACER is graph neural network for local prediction of protein-ligand conformational ensembles. - baker-laboratory/PLACER
github.com
February 13, 2025 at 8:28 PM
We are happy to share that the code and weights of PLACER (formerly known as ChemNet) are now public!
This method allows for rapid evaluation of protein side chain and ligand conformational ensembles, with uses in ligand docking and enzyme evaluation.
github.com/baker-labora...
This method allows for rapid evaluation of protein side chain and ligand conformational ensembles, with uses in ligand docking and enzyme evaluation.
github.com/baker-labora...