Patrick Barendse
@patrickbarendse.bsky.social
PhD candidate Biochemistry in the Swarts lab @WUR
Reposted by Patrick Barendse
BindCraft can be used to design synthetic protein binders with incredible accuracy and success rate - Out now in Nature.
BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.
BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 28, 2025 at 9:03 AM
BindCraft can be used to design synthetic protein binders with incredible accuracy and success rate - Out now in Nature.
BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.
BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.
Reposted by Patrick Barendse
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Patrick Barendse
Out now: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA
cell.com/molecular-ce...
Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?
cell.com/molecular-ce...
Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?
May 13, 2025 at 7:41 AM
Out now: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA
cell.com/molecular-ce...
Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?
cell.com/molecular-ce...
Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?
Reposted by Patrick Barendse
A PhD position is open for this year. A candidate should have a background in programming skills.
March 10, 2025 at 4:28 PM
A PhD position is open for this year. A candidate should have a background in programming skills.
Reposted by Patrick Barendse
#Argonautes2025 update ... it will happen this August (27-30) @imgprague.bsky.social. Our ITs are finishing and testing the website, the registration will open on March 1st. More info will be provided later (once all speakers reply to my e-mail, just saying, not pushing 😁). Poster announcement:
February 13, 2025 at 3:39 PM
#Argonautes2025 update ... it will happen this August (27-30) @imgprague.bsky.social. Our ITs are finishing and testing the website, the registration will open on March 1st. More info will be provided later (once all speakers reply to my e-mail, just saying, not pushing 😁). Poster announcement:
Reposted by Patrick Barendse
🚨New review🚨
Evolution and ecology of anti-defence systems in phages and plasmids
Link: www.cell.com/current-biol...
Evolution and ecology of anti-defence systems in phages and plasmids
Link: www.cell.com/current-biol...
January 7, 2025 at 10:27 AM
🚨New review🚨
Evolution and ecology of anti-defence systems in phages and plasmids
Link: www.cell.com/current-biol...
Evolution and ecology of anti-defence systems in phages and plasmids
Link: www.cell.com/current-biol...
Reposted by Patrick Barendse
Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems (cell.com/cell-reports...
It started with a simple question: Are certain prokaryotic immune systems always (or never) encoded with specific DNA repair proteins?...
It started with a simple question: Are certain prokaryotic immune systems always (or never) encoded with specific DNA repair proteins?...
January 7, 2025 at 8:46 AM
Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems (cell.com/cell-reports...
It started with a simple question: Are certain prokaryotic immune systems always (or never) encoded with specific DNA repair proteins?...
It started with a simple question: Are certain prokaryotic immune systems always (or never) encoded with specific DNA repair proteins?...
New paper alert!
Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems www.cell.com/cell-reports...
Together with @sumanthmutte.bsky.social, Pilar Bobadilla Ugarte, and Daan Swarts.
Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems www.cell.com/cell-reports...
Together with @sumanthmutte.bsky.social, Pilar Bobadilla Ugarte, and Daan Swarts.
January 6, 2025 at 2:55 PM
New paper alert!
Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems www.cell.com/cell-reports...
Together with @sumanthmutte.bsky.social, Pilar Bobadilla Ugarte, and Daan Swarts.
Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems www.cell.com/cell-reports...
Together with @sumanthmutte.bsky.social, Pilar Bobadilla Ugarte, and Daan Swarts.
Did you know that no natural inhibitors of prokaryotic Argonautes have been described (yet)? Together with @martinpacesa.bsky.social and Lennart Nickel, we designed our own de novo pAgo inhibitors! Check out these and other de novo protein designs in the updated Bindcraft preprint!
Additionally, we designed binders against another large nuclease – the prokaryotic Argonaute protein. Together with @patrickbarendse.bsky.social and Daan Swarts we show that are our binders can inhibit Argonaute cleavage activity!
December 8, 2024 at 10:22 AM
Did you know that no natural inhibitors of prokaryotic Argonautes have been described (yet)? Together with @martinpacesa.bsky.social and Lennart Nickel, we designed our own de novo pAgo inhibitors! Check out these and other de novo protein designs in the updated Bindcraft preprint!
Such a powerful protein binder design pipeline, and now with even more useful applications! Like guiding AAVs to specific cell surface receptors, neutralizing allergens, and inhibiting nucleases like Cas9 and pAgo!
We updated our BindCraft preprint with lots of new exciting results! We release all our binder sequences and models, include more in silico analysis, novel design targets, and present AAV retargeting to specific cell types using de novo binders!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 8, 2024 at 10:20 AM
Such a powerful protein binder design pipeline, and now with even more useful applications! Like guiding AAVs to specific cell surface receptors, neutralizing allergens, and inhibiting nucleases like Cas9 and pAgo!