AlphaFold and RosettaFold are deep learning models and are the state of the art in protein folding. That's one area where the tech has actually delivered. Of course, they're trained on protein structures, not just ChatGPT with a specific prompt.
November 17, 2025 at 2:05 PM
AlphaFold and RosettaFold are deep learning models and are the state of the art in protein folding. That's one area where the tech has actually delivered. Of course, they're trained on protein structures, not just ChatGPT with a specific prompt.
New Title Alert: RoseTTAFold2- a tool that extends the original three-track architecture of RoseTTAFold over the full network.
Learn more here: buff.ly/wQ22ZM2
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: buff.ly/wQ22ZM2
#SBGrid #SBGridSoftware #StructuralBiology
GitHub - uw-ipd/RoseTTAFold2
Contribute to uw-ipd/RoseTTAFold2 development by creating an account on GitHub.
buff.ly
November 7, 2025 at 5:31 PM
New Title Alert: RoseTTAFold2- a tool that extends the original three-track architecture of RoseTTAFold over the full network.
Learn more here: buff.ly/wQ22ZM2
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: buff.ly/wQ22ZM2
#SBGrid #SBGridSoftware #StructuralBiology
🔗 RoseTTAFold diffusion-guided short peptide design: a case study of binders against Keap1/Nrf2. Computational and Structural Biotechnology Journal, doi.org/10.1016/j.cs...
📚 CSBJ: www.csbj.org
#StructuralBiology #PeptideTherapeutics #RoseTTAFold #ProteinEngineering #MolecularDynamics #DrugDesign
📚 CSBJ: www.csbj.org
#StructuralBiology #PeptideTherapeutics #RoseTTAFold #ProteinEngineering #MolecularDynamics #DrugDesign
October 31, 2025 at 12:35 AM
🔗 RoseTTAFold diffusion-guided short peptide design: a case study of binders against Keap1/Nrf2. Computational and Structural Biotechnology Journal, doi.org/10.1016/j.cs...
📚 CSBJ: www.csbj.org
#StructuralBiology #PeptideTherapeutics #RoseTTAFold #ProteinEngineering #MolecularDynamics #DrugDesign
📚 CSBJ: www.csbj.org
#StructuralBiology #PeptideTherapeutics #RoseTTAFold #ProteinEngineering #MolecularDynamics #DrugDesign
Guys guys guys who wants to help answer this question?!:
"How have databases or algorithms designed to understand the way proteins fold, i.e. AlphaFold2 or RoseTTAFold, impacted your research?"
#biosky #RNAsky #structuralbiology #biophysics
"How have databases or algorithms designed to understand the way proteins fold, i.e. AlphaFold2 or RoseTTAFold, impacted your research?"
#biosky #RNAsky #structuralbiology #biophysics
October 29, 2025 at 1:07 AM
Guys guys guys who wants to help answer this question?!:
"How have databases or algorithms designed to understand the way proteins fold, i.e. AlphaFold2 or RoseTTAFold, impacted your research?"
#biosky #RNAsky #structuralbiology #biophysics
"How have databases or algorithms designed to understand the way proteins fold, i.e. AlphaFold2 or RoseTTAFold, impacted your research?"
#biosky #RNAsky #structuralbiology #biophysics
@nikomccarty.bsky.social , not recently active on #Bluesky, on the use of RosettaFold/biophysics in-silico modelling to design a "random walker" protein that is 10,000 times more efficient than naturally occurring equivalent ones.
October 6, 2025 at 9:32 AM
@nikomccarty.bsky.social , not recently active on #Bluesky, on the use of RosettaFold/biophysics in-silico modelling to design a "random walker" protein that is 10,000 times more efficient than naturally occurring equivalent ones.
Multistate and functional protein design using RoseTTAFold sequence space diffusion
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multistate and functional protein design using RoseTTAFold sequence space diffusion - Nature Biotechnology
ProteinGenerator simultaneously generates protein sequences and structures using sequence space diffusion.
www.nature.com
August 19, 2025 at 1:22 AM
Multistate and functional protein design using RoseTTAFold sequence space diffusion
www.nature.com/articles/s41...
www.nature.com/articles/s41...
RosettaFold 3 is here! 🧬🚀
AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!
Congratulations @simonmathis.bsky.social and team!!! ❤️
bioRxiv preprint: www.biorxiv.org/content/10.1...
AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!
Congratulations @simonmathis.bsky.social and team!!! ❤️
bioRxiv preprint: www.biorxiv.org/content/10.1...
August 15, 2025 at 1:26 PM
RosettaFold 3 is here! 🧬🚀
AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!
Congratulations @simonmathis.bsky.social and team!!! ❤️
bioRxiv preprint: www.biorxiv.org/content/10.1...
AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!
Congratulations @simonmathis.bsky.social and team!!! ❤️
bioRxiv preprint: www.biorxiv.org/content/10.1...
Some days I’m not sure I know what it *actually* means, and I’ve done it. I think? Maybe?
I should admit that my own knowledge of AI/ML is limited to the AlphaFold/RosettaFold class of models which, I believe, are fairly archaic in the scheme of things.
I should admit that my own knowledge of AI/ML is limited to the AlphaFold/RosettaFold class of models which, I believe, are fairly archaic in the scheme of things.
July 23, 2025 at 11:26 PM
Some days I’m not sure I know what it *actually* means, and I’ve done it. I think? Maybe?
I should admit that my own knowledge of AI/ML is limited to the AlphaFold/RosettaFold class of models which, I believe, are fairly archaic in the scheme of things.
I should admit that my own knowledge of AI/ML is limited to the AlphaFold/RosettaFold class of models which, I believe, are fairly archaic in the scheme of things.
Finally, we examined chemical foundation models, such as protein models (think AlphaFold/RoseTTAFold) and "universal" ML interatomic potentials. These models suffer from few of the ethical problems of general-purpose models like LLMs, but their environmental cost is still a cause for concern. (8/10)
July 7, 2025 at 1:12 PM
Finally, we examined chemical foundation models, such as protein models (think AlphaFold/RoseTTAFold) and "universal" ML interatomic potentials. These models suffer from few of the ethical problems of general-purpose models like LLMs, but their environmental cost is still a cause for concern. (8/10)
We hope this will catalyze progress towards even better models - like how CASP brought us to protein folding models like AlphaFold and RoseTTAFold. You can read about the Challenge in @cellpress.bsky.social
Commentary in Cell: www.cell.com/cell/fulltex...
Commentary in Cell: www.cell.com/cell/fulltex...
Virtual Cell Challenge: Toward a Turing test for the virtual cell
Virtual cells are an emerging frontier at the intersection of artificial intelligence
and biology. A key goal of these cell state models is predicting cellular responses
to perturbations. The Virtual ...
www.cell.com
June 26, 2025 at 3:30 PM
We hope this will catalyze progress towards even better models - like how CASP brought us to protein folding models like AlphaFold and RoseTTAFold. You can read about the Challenge in @cellpress.bsky.social
Commentary in Cell: www.cell.com/cell/fulltex...
Commentary in Cell: www.cell.com/cell/fulltex...
We find that a physics-based method (LUCS) samples greater structural diversity, approaching that observed in natural proteins, in a model protein fold than RFdiffusion, a generative model which utilizes the deep learning-based structure prediction network RoseTTAFold. (3/9)
June 10, 2025 at 6:28 PM
We find that a physics-based method (LUCS) samples greater structural diversity, approaching that observed in natural proteins, in a model protein fold than RFdiffusion, a generative model which utilizes the deep learning-based structure prediction network RoseTTAFold. (3/9)
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
Discover our Keypoint Blog on #NobelLaureate David Baker, who will deliver the closing Keynote at Keystone Symposia on #AI in Molecular Biology. Learn how AI is revolutionizing biomedical research!
#RoseTTAFold #keystonesymposia #KSAIBio26 bit.ly/42M5SlP @uwproteindesign.bsky.social
#RoseTTAFold #keystonesymposia #KSAIBio26 bit.ly/42M5SlP @uwproteindesign.bsky.social
Pioneering AI in Molecular Biology: Featuring nobel Laureate David Baker
Nobel Laureate David Baker will give the closing Keynote address at the upcoming Keystone Symposia meeting: AI in Molecular Biology, taking place September 15-18, in Santa Fe, New Mexico.
bit.ly
April 29, 2025 at 3:41 PM
Discover our Keypoint Blog on #NobelLaureate David Baker, who will deliver the closing Keynote at Keystone Symposia on #AI in Molecular Biology. Learn how AI is revolutionizing biomedical research!
#RoseTTAFold #keystonesymposia #KSAIBio26 bit.ly/42M5SlP @uwproteindesign.bsky.social
#RoseTTAFold #keystonesymposia #KSAIBio26 bit.ly/42M5SlP @uwproteindesign.bsky.social
3D structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these [2/7 of https://arxiv.org/abs/2504.14059v1]
April 22, 2025 at 6:15 AM
3D structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these [2/7 of https://arxiv.org/abs/2504.14059v1]
arXiv:2504.01490v1 Announce Type: new
Abstract: This systematic review outlines pivotal advancements in deep learning-driven protein structure prediction and design, focusing on four core models-AlphaFold, RoseTTAFold, RFDiffusion, and [1/6 of https://arxiv.org/abs/2504.01490v1]
Abstract: This systematic review outlines pivotal advancements in deep learning-driven protein structure prediction and design, focusing on four core models-AlphaFold, RoseTTAFold, RFDiffusion, and [1/6 of https://arxiv.org/abs/2504.01490v1]
April 3, 2025 at 6:12 AM
arXiv:2504.01490v1 Announce Type: new
Abstract: This systematic review outlines pivotal advancements in deep learning-driven protein structure prediction and design, focusing on four core models-AlphaFold, RoseTTAFold, RFDiffusion, and [1/6 of https://arxiv.org/abs/2504.01490v1]
Abstract: This systematic review outlines pivotal advancements in deep learning-driven protein structure prediction and design, focusing on four core models-AlphaFold, RoseTTAFold, RFDiffusion, and [1/6 of https://arxiv.org/abs/2504.01490v1]
AlphaFold3 and RoseTTAFold All-Atom structures enable radiosensitizers discovery by targeting multiple DNA damage repair proteins https://www.biorxiv.org/content/10.1101/2025.03.26.645385v1
March 30, 2025 at 2:48 AM
AlphaFold3 and RoseTTAFold All-Atom structures enable radiosensitizers discovery by targeting multiple DNA damage repair proteins https://www.biorxiv.org/content/10.1101/2025.03.26.645385v1
AlphaFold3 and RoseTTAFold All-Atom structures enable radiosensitizers discovery by targeting multiple DNA damage repair proteins https://www.biorxiv.org/content/10.1101/2025.03.26.645385v1
March 30, 2025 at 2:48 AM
AlphaFold3 and RoseTTAFold All-Atom structures enable radiosensitizers discovery by targeting multiple DNA damage repair proteins https://www.biorxiv.org/content/10.1101/2025.03.26.645385v1
We evaluate 6 leading protein structure predictors—AlphaFold 2 and 3, Boltz-1, ESMFold, OmegaFold, and RoseTTAFold 2—on the 10 known sactipeptides.
All models exhibit limited performance, with an average GDT-TS of only 11.5% for known sactipeptides and 12.6% for unknown ones.
All models exhibit limited performance, with an average GDT-TS of only 11.5% for known sactipeptides and 12.6% for unknown ones.
March 27, 2025 at 8:18 PM
We evaluate 6 leading protein structure predictors—AlphaFold 2 and 3, Boltz-1, ESMFold, OmegaFold, and RoseTTAFold 2—on the 10 known sactipeptides.
All models exhibit limited performance, with an average GDT-TS of only 11.5% for known sactipeptides and 12.6% for unknown ones.
All models exhibit limited performance, with an average GDT-TS of only 11.5% for known sactipeptides and 12.6% for unknown ones.
How are you defining “non-AI” in this case? Methods like AlphaFold and RosettaFold definitely fall in the “AI” bucket, even if they take a different algorithmic approach than LLMs.
March 26, 2025 at 11:25 PM
How are you defining “non-AI” in this case? Methods like AlphaFold and RosettaFold definitely fall in the “AI” bucket, even if they take a different algorithmic approach than LLMs.
As someone who use to study proteins but stopped the year #AlphaFold and #RoseTTAfold hid the scene I wonder how studying proteins has changed since.
What is the impact on your work of having all those protein structures availible?
🧪 #Protein
What is the impact on your work of having all those protein structures availible?
🧪 #Protein
March 21, 2025 at 9:27 AM
As someone who use to study proteins but stopped the year #AlphaFold and #RoseTTAfold hid the scene I wonder how studying proteins has changed since.
What is the impact on your work of having all those protein structures availible?
🧪 #Protein
What is the impact on your work of having all those protein structures availible?
🧪 #Protein
structure prediction via AlphaFold2, RoseTTAFold, ESMFold, and others have achieved near-experimental accuracy, inspiring successive work extended to biomolecular complexes via AlphaFold Multimer, RoseTTAFold All-Atom, [2/9 of https://arxiv.org/abs/2502.19173v1]
February 27, 2025 at 6:12 AM
structure prediction via AlphaFold2, RoseTTAFold, ESMFold, and others have achieved near-experimental accuracy, inspiring successive work extended to biomolecular complexes via AlphaFold Multimer, RoseTTAFold All-Atom, [2/9 of https://arxiv.org/abs/2502.19173v1]
“Drug Discovery Startup Protai, AlphaFold, Proteomik ve NVIDIA NIM ile Karmaşık Yapı Tahminini Geliştiriyor”
Üretken Yapay Zeka, AlphaFold ve RosettaFold gibi olağanüstü ilerlemelerle, ilaç keşif süreçlerini dönüştürmektedir. Biyoteknoloji şirketleri ve araştırma laboratuvarları protein yapılarını…
Üretken Yapay Zeka, AlphaFold ve RosettaFold gibi olağanüstü ilerlemelerle, ilaç keşif süreçlerini dönüştürmektedir. Biyoteknoloji şirketleri ve araştırma laboratuvarları protein yapılarını…
“Drug Discovery Startup Protai, AlphaFold, Proteomik ve NVIDIA NIM ile Karmaşık Yapı Tahminini Geliştiriyor”
Üretken Yapay Zeka, AlphaFold ve RosettaFold gibi olağanüstü ilerlemelerle, ilaç keşif süreçlerini dönüştürmektedir. Biyoteknoloji şirketleri ve araştırma laboratuvarları protein yapılarını incelerken, protein etkileşimleri hakkında devrim niteliğinde bilgiler elde etmektedir. Proteinler dinamik varlıklardır. Bir proteinin doğal durumu yalnızca amino asit dizilimi tarafından belirlenir; örneğin AlphaFold2 ve Uygulamaları üzerine yapılan araştırmalarda bu durum ortaya konmuştur. Ancak tek bir protein, çevresel koşullara bağlı olarak farklı yapısal konformasyonlar benimseyebilir.
wm.org.tr
February 19, 2025 at 6:58 PM
“Drug Discovery Startup Protai, AlphaFold, Proteomik ve NVIDIA NIM ile Karmaşık Yapı Tahminini Geliştiriyor”
Üretken Yapay Zeka, AlphaFold ve RosettaFold gibi olağanüstü ilerlemelerle, ilaç keşif süreçlerini dönüştürmektedir. Biyoteknoloji şirketleri ve araştırma laboratuvarları protein yapılarını…
Üretken Yapay Zeka, AlphaFold ve RosettaFold gibi olağanüstü ilerlemelerle, ilaç keşif süreçlerini dönüştürmektedir. Biyoteknoloji şirketleri ve araştırma laboratuvarları protein yapılarını…
Ignore the click baity headline and opening - this is a *really* good description of the two parts of the 2024 Chemistry Nobel prize: predicting a protein structure from its sequence (AlphaFold) and designing a protein to have a function (Baker lab: RoseTTAFold diffusion); and their huge potential.
The Most Useful Thing AI Has Done
YouTube video by Veritasium
youtu.be
February 13, 2025 at 7:42 AM
Ignore the click baity headline and opening - this is a *really* good description of the two parts of the 2024 Chemistry Nobel prize: predicting a protein structure from its sequence (AlphaFold) and designing a protein to have a function (Baker lab: RoseTTAFold diffusion); and their huge potential.