3/18 However, optimization-based methods are expensive and time-consuming. BindCraft is the most famous approach, combining multiple models to design binders (ie. proteins that interact with target proteins)
bsky.app/profile/mian...
bsky.app/profile/mian...
1/13 🧵 Today, Bindcraft was published in
@nature.com , one of the most famous AIs in biology for designing protein–protein interactions (PPI). In my opinion. Bindcraft represents one of the most important advances in the post–AlphaFold2 era.
@nature.com , one of the most famous AIs in biology for designing protein–protein interactions (PPI). In my opinion. Bindcraft represents one of the most important advances in the post–AlphaFold2 era.
November 4, 2026 at 10:02 PM
3/18 However, optimization-based methods are expensive and time-consuming. BindCraft is the most famous approach, combining multiple models to design binders (ie. proteins that interact with target proteins)
bsky.app/profile/mian...
bsky.app/profile/mian...
Chaperone (Baker lab, IPD) wires 50+ protein design, folding and analysis tools (RFD3, BindCraft, AF3...) into reproducible SLURM pipelines, with agent skills so coding agents can run design campaigns. MIT license.
Details: toolome.bio/tools/chaperone/ #ProteinDesign #AIAgents
Details: toolome.bio/tools/chaperone/ #ProteinDesign #AIAgents
October 26, 2026 at 3:17 AM
Chaperone (Baker lab, IPD) wires 50+ protein design, folding and analysis tools (RFD3, BindCraft, AF3...) into reproducible SLURM pipelines, with agent skills so coding agents can run design campaigns. MIT license.
Details: toolome.bio/tools/chaperone/ #ProteinDesign #AIAgents
Details: toolome.bio/tools/chaperone/ #ProteinDesign #AIAgents
Protein is the largest category on Toolome: 54 of 293 tools. MIT 20, Apache-2.0 12, BSD-3-Clause 9, other 13; 2024 had the most first releases (11). Featured: ProteinMPNN, ESM-2 / ESMFold, RFdiffusion, BindCraft, Boltz. toolome.bio
October 18, 2026 at 3:23 PM
Protein is the largest category on Toolome: 54 of 293 tools. MIT 20, Apache-2.0 12, BSD-3-Clause 9, other 13; 2024 had the most first releases (11). Featured: ProteinMPNN, ESM-2 / ESMFold, RFdiffusion, BindCraft, Boltz. toolome.bio
Technical Notes: This month's software push includes updates to 11 titles -- Amber, BindCraft, ChemEx, HTSlib, IMOD, NAMD, Octopi, Picard, PolNet, PowerFit, and Warp.
More here: buff.ly/7vPHwES
#SBGrid #Software #StructuralBiology
More here: buff.ly/7vPHwES
#SBGrid #Software #StructuralBiology
SBGrid Consortium - Software Updates
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
buff.ly
October 7, 2026 at 4:04 PM
Technical Notes: This month's software push includes updates to 11 titles -- Amber, BindCraft, ChemEx, HTSlib, IMOD, NAMD, Octopi, Picard, PolNet, PowerFit, and Warp.
More here: buff.ly/7vPHwES
#SBGrid #Software #StructuralBiology
More here: buff.ly/7vPHwES
#SBGrid #Software #StructuralBiology
Want the full picture? It's all here:
Overview + modalities: pacesalab.com/bindcraft
Wiki + design guide: github.com/PacesaLab/Bi...
Run it now on Colab: colab.research.google.com/github/Paces...
Overview + modalities: pacesalab.com/bindcraft
Wiki + design guide: github.com/PacesaLab/Bi...
Run it now on Colab: colab.research.google.com/github/Paces...
BindCraft2 | Pacesa Lab
BindCraft2 is the next generation of our platform for user-friendly de novo protein binder design. Like the original, it was built to make binder design easy…
pacesalab.com
September 21, 2026 at 9:55 AM
Want the full picture? It's all here:
Overview + modalities: pacesalab.com/bindcraft
Wiki + design guide: github.com/PacesaLab/Bi...
Run it now on Colab: colab.research.google.com/github/Paces...
Overview + modalities: pacesalab.com/bindcraft
Wiki + design guide: github.com/PacesaLab/Bi...
Run it now on Colab: colab.research.google.com/github/Paces...
Anthropic has used Claude to optimise structure prediction and design code to improve speed and memory efficiency. 2-3X speed improvements on AF3, 5X on OF3, 5X on BindCraft low memory modes to model large assemblies. All released as open source
www.anthropic.com/research/cla...
www.anthropic.com/research/cla...
How Claude is uplifting biomolecular modeling
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
www.anthropic.com
September 18, 2026 at 9:54 AM
Anthropic has used Claude to optimise structure prediction and design code to improve speed and memory efficiency. 2-3X speed improvements on AF3, 5X on OF3, 5X on BindCraft low memory modes to model large assemblies. All released as open source
www.anthropic.com/research/cla...
www.anthropic.com/research/cla...
2️⃣1️⃣ 300,000 in silico protein binder candidates generated with BindCraft, covering more than 8,000 human protein targets.
bindome.epfl.ch/static/index...
bindome.epfl.ch/static/index...
Bindome Database
Bindome provides over 300,000 in silico protein binder candidates generated with BindCraft, covering more than 8,000 human protein targets.
bindome.epfl.ch
August 26, 2026 at 12:14 PM
2️⃣1️⃣ 300,000 in silico protein binder candidates generated with BindCraft, covering more than 8,000 human protein targets.
bindome.epfl.ch/static/index...
bindome.epfl.ch/static/index...
A collaborative team have published #BindCraft, an AI tool that designs powerful protein binders in one shot.
Critical for faster drugs, smarter diagnostics, and biotech breakthroughs ahead. www.nature.com/articles/s41...
Critical for faster drugs, smarter diagnostics, and biotech breakthroughs ahead. www.nature.com/articles/s41...
August 29, 2025 at 6:57 AM
A collaborative team have published #BindCraft, an AI tool that designs powerful protein binders in one shot.
Critical for faster drugs, smarter diagnostics, and biotech breakthroughs ahead. www.nature.com/articles/s41...
Critical for faster drugs, smarter diagnostics, and biotech breakthroughs ahead. www.nature.com/articles/s41...
12/13 🧵
"Leo, I use RFdiffusion or BoltzGen for my binder design. Is IARA useful?" Yes! The principles BindCraft uses are shared among these generative models, so IARA can be used alongside those tools too.
"Leo, I use RFdiffusion or BoltzGen for my binder design. Is IARA useful?" Yes! The principles BindCraft uses are shared among these generative models, so IARA can be used alongside those tools too.
April 17, 2026 at 10:10 AM
12/13 🧵
"Leo, I use RFdiffusion or BoltzGen for my binder design. Is IARA useful?" Yes! The principles BindCraft uses are shared among these generative models, so IARA can be used alongside those tools too.
"Leo, I use RFdiffusion or BoltzGen for my binder design. Is IARA useful?" Yes! The principles BindCraft uses are shared among these generative models, so IARA can be used alongside those tools too.
11/13 🧵
How good is IARA? Well, it rocks! It correctly predicts where BindCraft produces binders in synthetic proteins (unseen in training), on mammalian surface proteins, and on proteins with unnatural “dark folds” (Harteveld, Cell Systems 2024).
How good is IARA? Well, it rocks! It correctly predicts where BindCraft produces binders in synthetic proteins (unseen in training), on mammalian surface proteins, and on proteins with unnatural “dark folds” (Harteveld, Cell Systems 2024).
April 17, 2026 at 10:10 AM
11/13 🧵
How good is IARA? Well, it rocks! It correctly predicts where BindCraft produces binders in synthetic proteins (unseen in training), on mammalian surface proteins, and on proteins with unnatural “dark folds” (Harteveld, Cell Systems 2024).
How good is IARA? Well, it rocks! It correctly predicts where BindCraft produces binders in synthetic proteins (unseen in training), on mammalian surface proteins, and on proteins with unnatural “dark folds” (Harteveld, Cell Systems 2024).
3/13 🧵
I wondered if an ML model could learn the rationale behind BindCraft's binder design. For that, I needed to select a large number of targets to build a dataset of BindCraft runs.
I wondered if an ML model could learn the rationale behind BindCraft's binder design. For that, I needed to select a large number of targets to build a dataset of BindCraft runs.
April 17, 2026 at 10:10 AM
3/13 🧵
I wondered if an ML model could learn the rationale behind BindCraft's binder design. For that, I needed to select a large number of targets to build a dataset of BindCraft runs.
I wondered if an ML model could learn the rationale behind BindCraft's binder design. For that, I needed to select a large number of targets to build a dataset of BindCraft runs.
2/13 🧵 This research was inspired by how variable results can be after thousands of GPU hours using BindCraft. While for some targets I could generate hundreds of binders fast, for others (looking at you, AP2 µ2 subunit 😤), I had none after hundreds of hours of compute.
ALT:
media.tenor.com
April 17, 2026 at 10:10 AM
2/13 🧵 This research was inspired by how variable results can be after thousands of GPU hours using BindCraft. While for some targets I could generate hundreds of binders fast, for others (looking at you, AP2 µ2 subunit 😤), I had none after hundreds of hours of compute.
One-shot design of functional protein binders with BindCraft #bindcraft #protein #design #molecularmodeling #modeling #ppis #alphafold2
September 1, 2025 at 6:52 AM
I haven’t tried it. my day-to-day doesn’t use those tools that often. I can give it a go and let you know. I’m sure there will be uses that are helpful. I am very grateful for Alphafold, Boltz, RF diffusion, and BindCraft. They certainly have changed my day to day. There are other bottle necks now.
November 18, 2025 at 8:17 AM
I haven’t tried it. my day-to-day doesn’t use those tools that often. I can give it a go and let you know. I’m sure there will be uses that are helpful. I am very grateful for Alphafold, Boltz, RF diffusion, and BindCraft. They certainly have changed my day to day. There are other bottle necks now.
No prob. To be fair - all of this DL code for proteins has nightmare dependencies. My team struggle all the time, plus working out how to run it well and for it to play nicely on HPC is generally a struggle. BindCraft has generally got the thumbs up though!
October 23, 2024 at 12:43 PM
No prob. To be fair - all of this DL code for proteins has nightmare dependencies. My team struggle all the time, plus working out how to run it well and for it to play nicely on HPC is generally a struggle. BindCraft has generally got the thumbs up though!
August 27, 2025 at 4:49 PM
I know but it looks like a nice application of bindcraft. There are some interesting targets for me, I'll probably give it a try.
August 5, 2026 at 4:57 AM
I know but it looks like a nice application of bindcraft. There are some interesting targets for me, I'll probably give it a try.
August 5, 2026 at 4:52 AM
de novo protein binder design (bindcraft-like www.nature.com/articles/s41...) to generate binders against my proteins of interest.
My binders are expressed and soluble, a good start.
My binders are expressed and soluble, a good start.
November 5, 2025 at 11:53 AM
de novo protein binder design (bindcraft-like www.nature.com/articles/s41...) to generate binders against my proteins of interest.
My binders are expressed and soluble, a good start.
My binders are expressed and soluble, a good start.
July 26, 2025 at 9:50 AM
Boltz-1x
Chai-1
Protenix
AF2
AF3
Unifold
CombFold
ESMFold
D-I-TASSER
RosettaFold All-Atom
IgDesign
RFantibody
BindCraft
RoseTTAFold2NA
AFCluster
AntiFold
HighFold
BioEmu
DiffAb
AbMPNN
RFDiffusion
HyperMPNN
AntiBERTy
AF-Traj
AbGPT
Chai-1
Protenix
AF2
AF3
Unifold
CombFold
ESMFold
D-I-TASSER
RosettaFold All-Atom
IgDesign
RFantibody
BindCraft
RoseTTAFold2NA
AFCluster
AntiFold
HighFold
BioEmu
DiffAb
AbMPNN
RFDiffusion
HyperMPNN
AntiBERTy
AF-Traj
AbGPT
a man with glasses is holding his head in front of a computer monitor
ALT: a man with glasses is holding his head in front of a computer monitor
media.tenor.com
June 5, 2025 at 12:36 PM
Boltz-1x
Chai-1
Protenix
AF2
AF3
Unifold
CombFold
ESMFold
D-I-TASSER
RosettaFold All-Atom
IgDesign
RFantibody
BindCraft
RoseTTAFold2NA
AFCluster
AntiFold
HighFold
BioEmu
DiffAb
AbMPNN
RFDiffusion
HyperMPNN
AntiBERTy
AF-Traj
AbGPT
Chai-1
Protenix
AF2
AF3
Unifold
CombFold
ESMFold
D-I-TASSER
RosettaFold All-Atom
IgDesign
RFantibody
BindCraft
RoseTTAFold2NA
AFCluster
AntiFold
HighFold
BioEmu
DiffAb
AbMPNN
RFDiffusion
HyperMPNN
AntiBERTy
AF-Traj
AbGPT
An open-source AI platform to democratize protein design is.gd/iNCD9M
An open-source AI platform to democratize protein design
Since its release in 2024, the open-source platform BindCraft, developed at EPFL, has already disrupted the world of protein design. Physical interactions between proteins influence anything from cell...
is.gd
August 29, 2025 at 8:39 PM
An open-source AI platform to democratize protein design is.gd/iNCD9M
Finally, Messi teamed up with our newest student Daphne Kaxiras to explore a new avenue for antimalarial design. Using the structure as a guide, they used #BindCraft to design and validate a mini-protein binder that inhibits parasite invasion by blocking the formation of the moving junction! 🚫🦠
June 30, 2026 at 5:13 PM
Finally, Messi teamed up with our newest student Daphne Kaxiras to explore a new avenue for antimalarial design. Using the structure as a guide, they used #BindCraft to design and validate a mini-protein binder that inhibits parasite invasion by blocking the formation of the moving junction! 🚫🦠