Just before the New Year: BindCraft v1.5! Please fill out this form to request new features and help us make BindCraft even better.
forms.gle/XsGHDCyHtczV...
forms.gle/XsGHDCyHtczV...
December 30, 2024 at 9:35 PM
Just before the New Year: BindCraft v1.5! Please fill out this form to request new features and help us make BindCraft even better.
forms.gle/XsGHDCyHtczV...
forms.gle/XsGHDCyHtczV...
Nature research paper: One-shot design of functional protein binders with BindCraft
go.nature.com/46bhOAv
go.nature.com/46bhOAv
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.
go.nature.com
September 1, 2025 at 5:37 PM
Nature research paper: One-shot design of functional protein binders with BindCraft
go.nature.com/46bhOAv
go.nature.com/46bhOAv
Excellent nanomolar peptide design success rates with BindCraft!
Generative Design of High-Affinity Peptides Using BindCraft [new]
De novo designs peptide ligands for proteins. It generated MDM2 binders (nM affinity) and WDR5 binders (sub-µM affinity), with potency improved via stapling.
De novo designs peptide ligands for proteins. It generated MDM2 binders (nM affinity) and WDR5 binders (sub-µM affinity), with potency improved via stapling.
July 26, 2025 at 7:14 AM
Excellent nanomolar peptide design success rates with BindCraft!
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...
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
github.com/martinpacesa...
BindCraft: an AlphaFold2-powered de novo protein binder design tool 🧬✨
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.
www.nature.com
October 5, 2025 at 12:07 PM
BindCraft: an AlphaFold2-powered de novo protein binder design tool 🧬✨
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
New Title Alert: BindCraft- a user friendly and accurate binder design pipeline.
Learn more here: https://buff.ly/3CEqPpU
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: https://buff.ly/3CEqPpU
#SBGrid #SBGridSoftware #StructuralBiology
GitHub - martinpacesa/BindCraft: User friendly and accurate binder design pipeline
User friendly and accurate binder design pipeline. Contribute to martinpacesa/BindCraft development by creating an account on GitHub.
buff.ly
February 6, 2025 at 12:00 PM
New Title Alert: BindCraft- a user friendly and accurate binder design pipeline.
Learn more here: https://buff.ly/3CEqPpU
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: https://buff.ly/3CEqPpU
#SBGrid #SBGridSoftware #StructuralBiology
Really fun and challenging (!) discussion with @cdbahl.com on BindCraft, the state of binder design, the oustanding challenges and perhaps also some misconceptions in the field 💫
www.healthtech.com/the-chain/ma...
www.healthtech.com/the-chain/ma...
Episode 84 Martin Pacesa on BindCraft An Automated Pipeline for De Novo Protein Binder Design
April 14, 2026 | How is BindCraft, the automated pipeline for de novo protein binder design, changing the protein design industry? Martin Pacesa, assistant professor of pharmacology at the University ...
www.healthtech.com
April 14, 2026 at 2:12 PM
Really fun and challenging (!) discussion with @cdbahl.com on BindCraft, the state of binder design, the oustanding challenges and perhaps also some misconceptions in the field 💫
www.healthtech.com/the-chain/ma...
www.healthtech.com/the-chain/ma...
July 26, 2025 at 9:50 AM
I am pleased to announce the release of ProteinDJ v2! This is a major update that integrates BindCraft into the pipeline as an alternative to RFdiffusion for binder generation. You can try it out here: github.com/PapenfussLab/proteindj
#ProteinDJ #BindCraft #ProteinDesign @wehi-research.bsky.social
#ProteinDJ #BindCraft #ProteinDesign @wehi-research.bsky.social
November 25, 2025 at 3:01 AM
I am pleased to announce the release of ProteinDJ v2! This is a major update that integrates BindCraft into the pipeline as an alternative to RFdiffusion for binder generation. You can try it out here: github.com/PapenfussLab/proteindj
#ProteinDJ #BindCraft #ProteinDesign @wehi-research.bsky.social
#ProteinDJ #BindCraft #ProteinDesign @wehi-research.bsky.social
Take the BindCraft user survey to let us know how to improve the binder design protocol!
forms.gle/XsGHDCyHtczV...
forms.gle/XsGHDCyHtczV...
January 6, 2025 at 8:27 AM
Take the BindCraft user survey to let us know how to improve the binder design protocol!
forms.gle/XsGHDCyHtczV...
forms.gle/XsGHDCyHtczV...
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.
BindEnergyCraft claims to improve BindCraft performance using an energy-based objective.
"Code will be released soon."
"Code will be released soon."
May 30, 2025 at 7:43 PM
BindEnergyCraft claims to improve BindCraft performance using an energy-based objective.
"Code will be released soon."
"Code will be released soon."
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 8:27 AM
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...
This graced our journal club recently
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.
www.nature.com
October 3, 2025 at 5:24 PM
This graced our journal club recently
"Generative Design of High-Affinity Peptides Using BindCraft".
New @biorxivpreprint.bsky.social by the group of @sebastianpomplun.bsky.social of our @led3hub.bsky.social!
www.biorxiv.org/content/10.1...
Cc: @leidenscience.bsky.social, @unileiden.bsky.social
New @biorxivpreprint.bsky.social by the group of @sebastianpomplun.bsky.social of our @led3hub.bsky.social!
www.biorxiv.org/content/10.1...
Cc: @leidenscience.bsky.social, @unileiden.bsky.social
Generative Design of High-Affinity Peptides Using BindCraft
Discovering high-affinity ligands directly from protein structures remains a key challenge in drug discovery. We applied BindCraft, a structure-guided generative modeling platform, to de novo design o...
www.biorxiv.org
July 26, 2025 at 10:07 AM
"Generative Design of High-Affinity Peptides Using BindCraft".
New @biorxivpreprint.bsky.social by the group of @sebastianpomplun.bsky.social of our @led3hub.bsky.social!
www.biorxiv.org/content/10.1...
Cc: @leidenscience.bsky.social, @unileiden.bsky.social
New @biorxivpreprint.bsky.social by the group of @sebastianpomplun.bsky.social of our @led3hub.bsky.social!
www.biorxiv.org/content/10.1...
Cc: @leidenscience.bsky.social, @unileiden.bsky.social
What an amazing experience to be at the 76th Mosbacher kolloquim! Awesome talks on protein design and structural biology and a lot of conceptual discussions on where the field is going. Glad to also have been able to present our poster on binder design using BindCraft!
March 23, 2025 at 12:14 PM
What an amazing experience to be at the 76th Mosbacher kolloquim! Awesome talks on protein design and structural biology and a lot of conceptual discussions on where the field is going. Glad to also have been able to present our poster on binder design using BindCraft!
We plan to keep developing open source and user friendly software in the future, to put research tools into everyone's hands. You can find the easily installable BindCraft code on GitHub
github.com/martinpacesa...
github.com/martinpacesa...
GitHub - martinpacesa/BindCraft: User friendly and accurate binder design pipeline
User friendly and accurate binder design pipeline. Contribute to martinpacesa/BindCraft development by creating an account on GitHub.
github.com
August 27, 2025 at 4:14 PM
We plan to keep developing open source and user friendly software in the future, to put research tools into everyone's hands. You can find the easily installable BindCraft code on GitHub
github.com/martinpacesa...
github.com/martinpacesa...
Equivariance is dead! 😢
Or is it? 😈
Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa.
It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇
Or is it? 😈
Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa.
It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇
Introducing Genie 3, a generative protein model that substantially advances the state-of-the-art for binder design, increasing in silico success rates by up to 20x on hard multimeric targets. It also debuts a form of inference-time scaling unobserved in other design models. 🧵1/8
May 8, 2026 at 2:10 PM
Equivariance is dead! 😢
Or is it? 😈
Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa.
It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇
Or is it? 😈
Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa.
It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇
TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision www.biorxiv.org/content/10.1...
www.biorxiv.org
April 29, 2025 at 6:38 PM
TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision www.biorxiv.org/content/10.1...
Super excited about our 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕 pipeline being highlighted as one of @twistbioscience.com favourite publications of 2025!
We did synthesize all binder genes with Twist ❤️
We did synthesize all binder genes with Twist ❤️
BindCraft, an open-source and automated pipeline for de novo protein binder design is presented by Bruno Correia, Martin Pacesa, Lennart Nickel, and Christian Schellhaas:
“One-shot design of functional protein binders with BindCraft”
“One-shot design of functional protein binders with BindCraft”
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity wit...
www.nature.com
December 29, 2025 at 3:15 PM
Super excited about our 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕 pipeline being highlighted as one of @twistbioscience.com favourite publications of 2025!
We did synthesize all binder genes with Twist ❤️
We did synthesize all binder genes with Twist ❤️
Thank you to everyone for the support and @sokrypton.org for developing the code base which makes these updates much easier to do! Expect BindCraft v2 mid 2025!
github.com/martinpacesa...
github.com/martinpacesa...
GitHub - martinpacesa/BindCraft: User friendly and accurate binder design pipeline
User friendly and accurate binder design pipeline. Contribute to martinpacesa/BindCraft development by creating an account on GitHub.
github.com
December 30, 2024 at 9:35 PM
Thank you to everyone for the support and @sokrypton.org for developing the code base which makes these updates much easier to do! Expect BindCraft v2 mid 2025!
github.com/martinpacesa...
github.com/martinpacesa...
Very interesting technique, will certainly try!
Also great external validation of BindCraft, 7/36 binders bound, two with 0.8 and 6 nM affinity! Congratulations on the great work!
Also great external validation of BindCraft, 7/36 binders bound, two with 0.8 and 6 nM affinity! Congratulations on the great work!
You designed binders for your favourite protein and wish there was a way to experimentally screen them within 24h w/ only a set of pipettes and a plate reader?
Check out our Cell-Free 2-Hybrid approach (CF2H)
Full post: tinyurl.com/48cz5nb6
Preprint: www.biorxiv.org/cgi/content/...
Check out our Cell-Free 2-Hybrid approach (CF2H)
Full post: tinyurl.com/48cz5nb6
Preprint: www.biorxiv.org/cgi/content/...
July 18, 2025 at 9:38 AM
Very interesting technique, will certainly try!
Also great external validation of BindCraft, 7/36 binders bound, two with 0.8 and 6 nM affinity! Congratulations on the great work!
Also great external validation of BindCraft, 7/36 binders bound, two with 0.8 and 6 nM affinity! Congratulations on the great work!
BindCraft is now published in @nature.com!
The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.
Read more at GEN:
www.genengnews.com/topics/artif...
The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.
Read more at GEN:
www.genengnews.com/topics/artif...
BindCraft AI Model Achieves One-Shot Functional Protein Design
The open-source pipeline designs proteins with improved success rates for therapeutic targets, including gene editing proteins and allergens.
www.genengnews.com
August 27, 2025 at 4:55 PM
BindCraft is now published in @nature.com!
The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.
Read more at GEN:
www.genengnews.com/topics/artif...
The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.
Read more at GEN:
www.genengnews.com/topics/artif...