PhD student | Protein Designer
Joined August 2021
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Casper Goverde retweeted
Have you ever wanted to design protein binders with ease? Today we present 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕, a user-friendly and open-source pipeline that allows to anyone to create protein binders de novo with high experimental success rates. @befcorreia @sokrypton
biorxiv.org/content/10.1101/…
The last two years of my PhD I've worked with great pleasure with @MartinPacesa @GoldbachNico @befcorreia and many others. When we started this journey we had no idea where this project would lead us, so I feel deeply humbled that we managed to publish our work in Nature.
Today in @Nature we present the results of our exploration of the soluble protein universe and the design of functional soluble membrane proteins with @CasperGoverde @GoldbachNico @befcorreia 1/6
nature.com/articles/s41586-0…
Casper Goverde retweeted
Today in @Nature we present the results of our exploration of the soluble protein universe and the design of functional soluble membrane proteins with @CasperGoverde @GoldbachNico @befcorreia 1/6
nature.com/articles/s41586-0…
Casper Goverde retweeted
Our method for molecular linker design with diffusion models (DiffLinker) got published in @NatMachIntell 🥳
nature.com/articles/s42256-0…
Thanks a lot to our amazing coauthors @HannesStaerk Clément Vignac @rneschneuing @vgsatorras @pafrossard @wellingmax @mmbronstein @befcorreia
After three years of my PhD in the field of protein design, I got the opportunity to share my view on it thanks to this amazing collaboration with Dina Listov and Sarel Fleishman from @WeizmannScience Here is a tweetorial! Full review is available here: doi.org/10.1038/s41580-024-0…
Even though a lot of progress has been made, protein design is not solved. Methods for designing functional dynamic and complex proteins from scratch still remain an unsolved challenge. A combination of AI-driven and physics based models are most likely the solution here.
There is a lot of work to be done and an exciting road ahead! Tools for the design of therapeutics, biosensors and many other urgent applications are within grasp. I'm grateful for the opportunity to have worked on this review! Read more here: doi.org/10.1038/s41580-024-0…
Casper Goverde retweeted
New preprint! In this project spearheaded by Anthony Marchand and @St_Buckley we designed new chemically-induced protein interactions and experimentally validated three binders targeting Bcl2:Venetoclax, DB3:Progesterone and PDF1:Actinonin complexes.
biorxiv.org/content/10.1101/…
Casper Goverde retweeted
THEY SAID WE COULDN'T DO IT........well, no one actually said that. But in our updated manuscript with @CasperGoverde, @GoldbachNico, and @befcorreia we show you can now design soluble analogues of membrane proteins with preserved functional features!
biorxiv.org/content/10.1101/…
Incredible work by the Levy lab! Using AlphaFold2 to generate a database of the multimeric proteome. This collaboration easily ranks among my top favorites 😍 Happy to share our joint effort with the world 🌟
So happy to see our work published at @CellCellPress !
We added the quaternary structure dimension to proteome-wide, #AlphaFold2 predictions:
The published paper: sciencedirect.com/science/ar…
The original 🧵 (Two more experimental structures since!)
xitter.cf/ElevyLab/status/166819…
Casper Goverde retweeted
So happy to see our work published at @CellCellPress !
We added the quaternary structure dimension to proteome-wide, #AlphaFold2 predictions:
The published paper: sciencedirect.com/science/ar…
The original 🧵 (Two more experimental structures since!)
xitter.cf/ElevyLab/status/166819…
⚛️Protein structures are key to elucidating molecular details of cellular processes. #AlphaFold2 & others unveiled millions of tertiary structures, but these proteins' quaternary structures remain mostly a mystery. Here's how to bridge the gap. Thread👇 biorxiv.org/content/10.1101/…
Casper Goverde retweeted
New amazing research from the @befcorreia lab! @zanderharteveld and Alexandra explore protein topologies that have not been found in nature using a novel deep learning pipeline called Genesis
Exploring "dark matter" protein folds using deep learning biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
Casper Goverde retweeted
⚛️Protein structures are key to elucidating molecular details of cellular processes. #AlphaFold2 & others unveiled millions of tertiary structures, but these proteins' quaternary structures remain mostly a mystery. Here's how to bridge the gap. Thread👇 biorxiv.org/content/10.1101/…
Casper Goverde retweeted
Turns out @tomhanks was in town, but, unfortunately, was a bit out of reach.... so @CasperGoverde, with the magic of @Photoshop and a little generative ai, made the dream come true 😶🌫️
Casper Goverde retweeted
Lastly, confirmed that the soluble analogues maintain the intricate topology of the membrane folds using crystal structures. This allowed us to further explore the sequence space of membrane topologies and achieve a de facto fold expansion of the soluble space.
Casper Goverde retweeted
We tried to solubilize the claudin, rhomboid, and GPCR membrane folds. Using vanilla ProteinMPNN, we were not able to design soluble versions of these proteins, so @JustasDauparas trained a new version called SolubleMPNN resulted in many soluble designs of these folds.
