#proteindesign
I didn't even have time to digest the RFDiffusion3 paper and test it before it was already out of date with RFD4-proteina
I didn't even have time to digest the RFDiffusion3 paper and test it before it was already out of date with RFD4-proteina
October 27, 2026 at 3:19 PM
#proteindesign
I didn't even have time to digest the RFDiffusion3 paper and test it before it was already out of date with RFD4-proteina
I didn't even have time to digest the RFDiffusion3 paper and test it before it was already out of date with RFD4-proteina
Tool Duel: RFdiffusion2 scaffolds enzyme active sites. RFdiffusion3 does that too, plus binders to DNA, proteins and small molecules, all-atom, and is ~10x faster. BSD-3-Clause, Science 2026. Toolome didn't build either; details at toolome.bio/tools/rfdiffusion3/ #ProteinDesign #CompBio
October 24, 2026 at 3:18 PM
Tool Duel: RFdiffusion2 scaffolds enzyme active sites. RFdiffusion3 does that too, plus binders to DNA, proteins and small molecules, all-atom, and is ~10x faster. BSD-3-Clause, Science 2026. Toolome didn't build either; details at toolome.bio/tools/rfdiffusion3/ #ProteinDesign #CompBio
AI designs enzymes with atomic precision
David Baker's lab unveiled AI-designed proteases for disease-related proteins and RFdiffusion3 for atomic-level protein design. 🔬
David Baker's lab unveiled AI-designed proteases for disease-related proteins and RFdiffusion3 for atomic-level protein design. 🔬
October 22, 2026 at 2:43 PM
AI designs enzymes with atomic precision
David Baker's lab unveiled AI-designed proteases for disease-related proteins and RFdiffusion3 for atomic-level protein design. 🔬
David Baker's lab unveiled AI-designed proteases for disease-related proteins and RFdiffusion3 for atomic-level protein design. 🔬
Protein design just went atomic. RFdiffusion3, from David Baker's lab at the University of Washington, designs proteins atom by atom instead of residue by residue, and the enzymes it designed already work in the lab. The full paper just landed in Science.
October 21, 2026 at 2:05 AM
Protein design just went atomic. RFdiffusion3, from David Baker's lab at the University of Washington, designs proteins atom by atom instead of residue by residue, and the enzymes it designed already work in the lab. The full paper just landed in Science.
TECNOLOGIA. 🧬 RFdiffusion3, del laboratorio del Nobel David Baker.⚛️ Diseña átomo a átomo, no aminoácido a aminoácido.⚡ 10 veces más rápido que su antecesor.🔓 Código abierto y gratuito www.cronicadelhenares.com/2026/10/rfdi...
RFdiffusion3: la IA que diseña proteínas átomo a átomo
El laboratorio del Nobel David Baker publica en Science un modelo que diseña proteínas átomo a átomo. Código abierto y diez veces más rápido.
www.cronicadelhenares.com
October 19, 2026 at 3:16 PM
TECNOLOGIA. 🧬 RFdiffusion3, del laboratorio del Nobel David Baker.⚛️ Diseña átomo a átomo, no aminoácido a aminoácido.⚡ 10 veces más rápido que su antecesor.🔓 Código abierto y gratuito www.cronicadelhenares.com/2026/10/rfdi...
2/ RFdiffusion3 flips that. Each amino acid is modeled as up to 14 atoms, and the model generates the protein together with whatever it has to touch: a small molecule, a strand of DNA, a metal ion. Nothing is designed in isolation, so the chemistry must fit from the start.
October 21, 2026 at 2:05 AM
2/ RFdiffusion3 flips that. Each amino acid is modeled as up to 14 atoms, and the model generates the protein together with whatever it has to touch: a small molecule, a strand of DNA, a metal ion. Nothing is designed in isolation, so the chemistry must fit from the start.
👍Atomic functional site scaffolding in biopolymers with RFdiffusion3 | Science www.science.org/doi/10.1126/...
Atomic functional site scaffolding in biopolymers with RFdiffusion3
The catalytic and other sophisticated functions of biomolecules arise from the placement of many atoms in three-dimensional space. Here, we describe a generative artificial intelligence method for bio...
www.science.org
October 20, 2026 at 1:12 AM
👍Atomic functional site scaffolding in biopolymers with RFdiffusion3 | Science www.science.org/doi/10.1126/...
Discover how the new RFdiffusion3 protein design AI models individual atoms to generate unprecedented structures, advancing biological chemical reactions.
#RFdiffusion3 #ProteinDesign #GenerativeAI #DavidBaker #Nvidia #AlphaFold3
#RFdiffusion3 #ProteinDesign #GenerativeAI #DavidBaker #Nvidia #AlphaFold3
RFdiffusion3 Protein Design AI Built at Atomic Level
RFdiffusion3 AI System Transforms Protein Design at the Atomic Level Researchers recently unveiled the detailed design scheme for RFdiffusion3. This generative artificial intelligence system constructs proteins and nucleic acids atom by atom. Moreover, proteins crafted through this new system successfully perform intended functions during actual chemical reactions. An international research team built this precise atomic modeling tool. Members include scientists from the University of Washington, Oxford University, and Nvidia.
dailytechnow.com
October 19, 2026 at 4:20 AM
Discover how the new RFdiffusion3 protein design AI models individual atoms to generate unprecedented structures, advancing biological chemical reactions.
#RFdiffusion3 #ProteinDesign #GenerativeAI #DavidBaker #Nvidia #AlphaFold3
#RFdiffusion3 #ProteinDesign #GenerativeAI #DavidBaker #Nvidia #AlphaFold3
David Bakerの最新論文（Scienceのほう）。これまではアミノ酸ベースで拡散モデルを使っていたが、原子レベルで拡散モデルを適用することで、核酸や金属配位酵素、低分子化合物やそれらの相互作用まで予測できるRFdiffusion3を開発！
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Atomic functional site scaffolding in biopolymers with RFdiffusion3
The catalytic and other sophisticated functions of biomolecules arise from the placement of many atoms in three-dimensional space. Here, we describe a generative artificial intelligence method for bio...
www.science.org
October 17, 2026 at 5:47 AM
David Bakerの最新論文（Scienceのほう）。これまではアミノ酸ベースで拡散モデルを使っていたが、原子レベルで拡散モデルを適用することで、核酸や金属配位酵素、低分子化合物やそれらの相互作用まで予測できるRFdiffusion3を開発！
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Atomic functional site scaffolding in biopolymers with RFdiffusion3 | Science
Atomic functional site scaffolding in biopolymers with RFdiffusion3
The catalytic and other sophisticated functions of biomolecules arise from the placement of many atoms in three-dimensional space. Here, we describe a generative artificial intelligence method for biopolymers, RFdiffusion3 (RFD3), which employs free atom ...
www.science.org
October 16, 2026 at 5:01 AM
Atomic functional site scaffolding in biopolymers with RFdiffusion3 | Science
Computational design of metalloproteases
->Nature | More on "Computational design of metalloproteins" at BigEarthData.ai
->Nature | More on "Computational design of metalloproteins" at BigEarthData.ai
Computational design of metalloproteases
Studer, S. et al. Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science 362, 1285–1288 (2018). Kim, D. et al. Computational design of metallohydrolases. Nature 649, 246–253 (2026). Bauer, M. S. et al. design of phospho-tyrosine peptide binders. Preprint at bioRxiv https://doi.org/10.1101/2025.09.29.678898 (2025). Butcher, J. et al. Design of all-atom biomolecular interactions with RFdiffusion3. Preprint at bioRxiv https://doi.org/10.1101/2025.09.18.676967 (2025). Radzicka, A. & Richard, W. Rates of uncatalyzed peptide bond hydrolysis in neutral solution and the transition state affinities of proteases. J. Am. Chem. Soc. 118, 6105–6109 (1996). Hooper, N. M. Families of zinc metalloproteases. FEBS Lett. 354, 1–6 (1994). Lipscomb, W. N. & Sträter, N. Recent advances in zinc enzymology. Chem. Rev. 96, 2375–2434 (1996). de Almeida, L. G. N. et al. Matrix metalloproteinases: from molecular mechanisms to physiology, pathophysiology, and pharmacology. Pharmacol. Rev. 74, 714–770 (2022). Page-McCaw, A., Ewald, A. J. & Werb, Z. Matrix metalloproteinases and the regulation of tissue remodelling. Nat. Rev. Mol. Cell Biol. 8, 221–233 (2007). Edwards, D. R., Handsley, M. M. & Pennington, C. J. The ADAM metalloproteinases. Mol. Aspects Med. 29, 258–289 (2008). Wang, Z., Li, W., Chen, S. & Tang, X. X. Role of ADAM and ADAMTS proteases in...
www.nature.com
October 15, 2026 at 10:26 AM
Our new Enzyme Design with RFdiffusion3 Tutorial walks step-by-step through a basic enzyme design workflow—from cropping a metallohydrolase PDB active site into a theozyme to writing the JSON input file for RFD3 inference. Check it out here: youtu.be/htA3HSXCkro #TutorialTuesday
October 13, 2026 at 1:00 PM
Our new Enzyme Design with RFdiffusion3 Tutorial walks step-by-step through a basic enzyme design workflow—from cropping a metallohydrolase PDB active site into a theozyme to writing the JSON input file for RFD3 inference. Check it out here: youtu.be/htA3HSXCkro #TutorialTuesday
This video is somewhat dry, but the fact that this is doable on consumer hardware, and you can order synthesized DNA for your proteins for like ~$100, truly gives me so much hope for the future.
I think we're going to see a lot of really cool biotech in the next few years :)
youtu.be/htA3HSXCkro
I think we're going to see a lot of really cool biotech in the next few years :)
youtu.be/htA3HSXCkro
Enzyme design with RFdiffusion3
YouTube video by RosettaCommons
youtu.be
October 9, 2026 at 3:45 AM
This video is somewhat dry, but the fact that this is doable on consumer hardware, and you can order synthesized DNA for your proteins for like ~$100, truly gives me so much hope for the future.
I think we're going to see a lot of really cool biotech in the next few years :)
youtu.be/htA3HSXCkro
I think we're going to see a lot of really cool biotech in the next few years :)
youtu.be/htA3HSXCkro
RFDiffusion3 simple motif scaffolding tutorials are here!
Follow along with this RFDiffusion3 video tutorial to learn how to design an entirely new scaffold to preserve a catalytic structural motif extracted from a known protein structure. www.youtube.com/watch?v=bFSW...
Follow along with this RFDiffusion3 video tutorial to learn how to design an entirely new scaffold to preserve a catalytic structural motif extracted from a known protein structure. www.youtube.com/watch?v=bFSW...
August 13, 2026 at 1:00 PM
RFDiffusion3 simple motif scaffolding tutorials are here!
Follow along with this RFDiffusion3 video tutorial to learn how to design an entirely new scaffold to preserve a catalytic structural motif extracted from a known protein structure. www.youtube.com/watch?v=bFSW...
Follow along with this RFDiffusion3 video tutorial to learn how to design an entirely new scaffold to preserve a catalytic structural motif extracted from a known protein structure. www.youtube.com/watch?v=bFSW...
De novo design of All-atom biomolecular interactions with RFdiffusion3 www.biorxiv.org/content/10.1...
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present RFd...
www.biorxiv.org
September 19, 2025 at 10:32 AM
De novo design of All-atom biomolecular interactions with RFdiffusion3 www.biorxiv.org/content/10.1...
6/7 We made a colab notebook demo where users can design ‘mini binders’ against human erythropoietin (hEPO) by integrating GlycoShape with the RFdiffusion3 (RFD3) pipeline (doi.org/10.1101/2025...) from the Institute for Protein Design (IDP) colab.research.google.com/github/Ojas-...
April 17, 2026 at 11:33 AM
6/7 We made a colab notebook demo where users can design ‘mini binders’ against human erythropoietin (hEPO) by integrating GlycoShape with the RFdiffusion3 (RFD3) pipeline (doi.org/10.1101/2025...) from the Institute for Protein Design (IDP) colab.research.google.com/github/Ojas-...
RFdiffusion3: One DNA binder tested (5.89 µM affinity, no specificity controls). 35/190 enzymes active (no catalytically-dead mutants).
RFdiffusion1 had cryo-EM structures and nM binders. RFdiffusion2 had crystal structures and mutagenesis.
medium.com/@enginyapici...
#ProteinDesign #DNABinding
RFdiffusion1 had cryo-EM structures and nM binders. RFdiffusion2 had crystal structures and mutagenesis.
medium.com/@enginyapici...
#ProteinDesign #DNABinding
RFdiffusion3: Atom-Level Protein Design at Scale
Baker Lab released RFdiffusion3, an all-atom diffusion model for designing proteins that interact with DNA, ligands, and other…
medium.com
January 14, 2026 at 3:56 PM
RFdiffusion3: One DNA binder tested (5.89 µM affinity, no specificity controls). 35/190 enzymes active (no catalytically-dead mutants).
RFdiffusion1 had cryo-EM structures and nM binders. RFdiffusion2 had crystal structures and mutagenesis.
medium.com/@enginyapici...
#ProteinDesign #DNABinding
RFdiffusion1 had cryo-EM structures and nM binders. RFdiffusion2 had crystal structures and mutagenesis.
medium.com/@enginyapici...
#ProteinDesign #DNABinding
The team at BioF:GREAT is always on the lookout for new protein design models that care about more than just the backbone! We are excited to try the new RFdiffusion3 (RFD3)! 🚀 New preprint from David Baker!🚀 🧪 #ProteinDesign #DeepLearning #ComputationalBiology
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present RFd...
www.biorxiv.org
September 19, 2025 at 3:15 PM
The team at BioF:GREAT is always on the lookout for new protein design models that care about more than just the backbone! We are excited to try the new RFdiffusion3 (RFD3)! 🚀 New preprint from David Baker!🚀 🧪 #ProteinDesign #DeepLearning #ComputationalBiology
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Naturally occurring enzymes, while powerful, catalyze only a fraction of the reactions chemists care about. That’s why scientists are eager to design new-to-nature versions that could carry out entirely new forms of chemistry that biology never evolved. cen.acs.org/physical-che...
#chemsky 🧪
#chemsky 🧪
A trio of AI methods tackles enzyme design
RFdiffusion2, RFdiffusion3, and Riff-Diff each solve different structural problems in computational enzyme design
cen.acs.org
January 4, 2026 at 10:17 AM
Naturally occurring enzymes, while powerful, catalyze only a fraction of the reactions chemists care about. That’s why scientists are eager to design new-to-nature versions that could carry out entirely new forms of chemistry that biology never evolved. cen.acs.org/physical-che...
#chemsky 🧪
#chemsky 🧪
Three new papers report improvements to enzyme design using diffusion models, a class of generative artificial intelligence algorithms that add and then subtract noise. cen.acs.org/physical-che... #chemsky 🧪
A trio of AI methods tackles enzyme design
RFdiffusion2, RFdiffusion3, and Riff-Diff each solve different structural problems in computational enzyme design
cen.acs.org
December 11, 2025 at 2:23 PM
Three new papers report improvements to enzyme design using diffusion models, a class of generative artificial intelligence algorithms that add and then subtract noise. cen.acs.org/physical-che... #chemsky 🧪
To illustrate the workflow we use, we set-up a colab notebook demo (colab.research.google.com/github/Ojas-...) where users can design ‘mini binders’ against human erythropoietin (hEPO) by integrating GlycoShape resources with the RFdiffusion3 (RFD3) pipeline
April 17, 2026 at 11:53 AM
To illustrate the workflow we use, we set-up a colab notebook demo (colab.research.google.com/github/Ojas-...) where users can design ‘mini binders’ against human erythropoietin (hEPO) by integrating GlycoShape resources with the RFdiffusion3 (RFD3) pipeline
Sometimes the hardest part of working with new tools is installing them. Watch this helpful tutorial to learn how to install RFDisffusion3 with Foundry so you can start experimenting with protein design today. www.youtube.com/watch?v=6rFE... #rcmegathon #rctutorial
July 21, 2026 at 12:00 PM
Sometimes the hardest part of working with new tools is installing them. Watch this helpful tutorial to learn how to install RFDisffusion3 with Foundry so you can start experimenting with protein design today. www.youtube.com/watch?v=6rFE... #rcmegathon #rctutorial
RFdiffusion3 is a powerful tool for binder design. The newest tutorial from Rosetta Commons provides step-by-step guidance for how to design binders for simple proteins, small molecules, and proteins with post-translational modifications. www.youtube.com/watch?v=q1tS...
#rcmegathon #rctutorial
#rcmegathon #rctutorial
July 14, 2026 at 4:54 PM
RFdiffusion3 is a powerful tool for binder design. The newest tutorial from Rosetta Commons provides step-by-step guidance for how to design binders for simple proteins, small molecules, and proteins with post-translational modifications. www.youtube.com/watch?v=q1tS...
#rcmegathon #rctutorial
#rcmegathon #rctutorial
Three RFdiffusion3 (RFD3) tutorials are now available. These tutorials walk you through how to use RFD3 to generate structures for: protein-protein interface design, enzyme design, and nucleic acid binder design, and can be expanded to other areas of interest. Check them out @ zurl.co/og3XK
April 2, 2026 at 2:01 PM
Three RFdiffusion3 (RFD3) tutorials are now available. These tutorials walk you through how to use RFD3 to generate structures for: protein-protein interface design, enzyme design, and nucleic acid binder design, and can be expanded to other areas of interest. Check them out @ zurl.co/og3XK
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3 www.biorxiv.org/content/10.1... 🧬🖥️🧪
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present…
www.biorxiv.org
September 19, 2025 at 3:55 PM
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3 www.biorxiv.org/content/10.1... 🧬🖥️🧪