Latest posts tagged with #RFdiffusion on Bluesky
Other features for v2 include template-guidance for #Boltz-2 prediction, auto-contig generation for #RFdiffusion, and models for #HyperMPNN. We have also made bug fixes, improvements to documentation, container updates and more. Details here: github.com/PapenfussLab/proteindj/releases/tag/v2.0.0
Atomically accurate de novo design of antibodies with RFdiffusion #antibody #design #modeling #rfdiffusion
ProteinDJ logo
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
Thanks to @biancabroske.bsky.social , @scbinder.bsky.social , @tim-kempchen.bsky.social and all the other authors for a fantastic collaboration. A big thank you goes to the developers of #RFdiffusion, #Chroma, #Bindcraft and others to make these amazing algorithms available.
When we saw the first tweats about #RFdiffusion and #Chroma, we wanted to try if we can apply these tools to our own research.
Have a look at our preprint and learn what worked out of the box and what didn't.
Finally read these 2 x papers from the Baker Lab (@uwproteindesign.bsky.social)🧬 De novo protein design for snake venom neutralisation (binders) 🐍 + multistep reactions (enzymes) 🧪 using #RFDiffusion.
nature.com/articles/s41...
science.org/doi/epdf/10.... #proteindesign #stucturalbiology #PhD
@biogrid.bsky.social is happy to release of our new themed curation project on #SyntheticProtein interactions using proteins generated with #rfdiffusion, #foldflow, and #bindcraft. Our page linked below contains all interactions and download files will be available very soon 🧪 #AI #MachineLearning
SciTech Chronicles. . . . . . . . .Feb 14th, 2025
bit.ly/stc021425
#perovskite #water first-generation #end-of-life #Titan #dissipation #rotation #circular #influenza #vaccine #H1N1 #H3N2 #proteins #enzymes #structure #RFdiffusion #buried #extremophiles #subglacial #hydrothermal
Cas activity assay. 3 strongest inhibitors characterised. Mimic RNAs. Xtallised one. Two others wouldn't xtallise, CD agrees with prediction; also checked folding/stability. Nice candidates for regulation of Cas. Functional in bacteria. Rescue phage infection as designed. As a crispr off switch - 8 weeks from AI design to targeted inhibitor.
Session 9 Cyntia Taveneau: De novo design of crispr-cas inhibitors. CRISPR system degrades DNA from phage; phage escape with antiCRISPR. Can we design them?? AIcrs designed to block active site of Cas13. #RFdiffusion Scoring top 96. Expr and purify. Biolayer interferometry. #LorneProteins2025
Toward #video #generative_models of the #molecular world
#AI #RFdiffusion #MDGen
phys.org/news/2025-01...
Antagonist antibodies can have unwanted agonist activities. It is now possible to generate pure antagonist protein-binding proteins with high affinity using RosettaFold | #Antibodies #TNFR #OX40 #4-1BB #RFdiffusion | David Baker uofwa.bsky.social | Science @science.org | tinyurl.com/yc34m5jt
I would appreciate any advice on analyzing a protein structure using #AlphaFold, Colab, or #RFDiffusion models to identify new interactors. If anyone is interested, I would love to connect via Teams and collaborate. 🧬🖥️ #deeplearning
I would appreciate any advice on analyzing a protein structure using #AlphaFold, Colab, or #RFDiffusion models to identify new interactors. If anyone is interested, I would love to connect via Teams and collaborate. 🧬🖥️ #deeplearning
We are open to various forms of collaboration and would value fluent feedback with expert groups in #AlphaFold Multimer and #RFDiffusion. Let’s connect! DM if you are interested!
We are exploring the structure of a protein using #AlphaFold and #RFDiffusion models to later identify potential interactors. Interested in collaborating? Please send a direct message. #AI #ML
Does anybody have an opinion on the benefits (or lack thereof) of the Ada generation (e.g. RTX 6000 Ada instead of RTX A6000) for a GPU workstation for AI tasks like #alphafold2 or #RFdiffusion?
Much attention has been focused on the de novo generation of protein binders using #RFDiffusion, #AlphaFold3 or #AlphaProteo. However, these models still need help with data scarcity, conformational changes, and hallucinations. (1/3
nature.com/articles/d4158…
Whenever possible, we employ emerging tools for protein design like #AlphaFold or #RFDiffusion. Still, many challenges are unique to peptides—short half-life, limited oral bioavailability, toxicity—and sampling bias and data scarcity to the #ML modelling process. (2/3
Protein Sequence Generation with EvoDiff: colbyford.medium.com/exploring-ai...
#proteins #diffusion #ai #computationalbiology #bioinformatics #rfdiffusion #alphafold #colabfold
