Philipp Becker
@philipp2907.bsky.social
PhD student @Schwille Lab in Munich. Protein Design for synthetic cells!
Reposted by Philipp Becker
With this, the last bit of my PhD at @embl.org is finally out!
We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models.
Paper: nature.com/articles/s42256-…
Code: github.com/mjendrusch/salad
Data: zenodo.org/records/14711580
1/🧵
We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models.
Paper: nature.com/articles/s42256-…
Code: github.com/mjendrusch/salad
Data: zenodo.org/records/14711580
1/🧵
‘Salad’ – a new AI model from EMBL scientists – offers major improvements in synthetic protein design.
Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields.
www.nature.com/articles/s42...
Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields.
www.nature.com/articles/s42...
September 24, 2025 at 12:27 PM
With this, the last bit of my PhD at @embl.org is finally out!
We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models.
Paper: nature.com/articles/s42256-…
Code: github.com/mjendrusch/salad
Data: zenodo.org/records/14711580
1/🧵
We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models.
Paper: nature.com/articles/s42256-…
Code: github.com/mjendrusch/salad
Data: zenodo.org/records/14711580
1/🧵
Reposted by Philipp Becker
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
July 7, 2025 at 8:21 AM
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Reposted by Philipp Becker
Can we build synthetic cells from de novo designed proteins?
Find out more in the latest review @natrevbioeng.nature.com from Bela Frohn, Shunshi Kohyama and Petra Schwille.
❕Publication: doi.org/10.1038/s442...
#ProteinDesign #SyntheticBiology @belafrohn.bsky.social
Find out more in the latest review @natrevbioeng.nature.com from Bela Frohn, Shunshi Kohyama and Petra Schwille.
❕Publication: doi.org/10.1038/s442...
#ProteinDesign #SyntheticBiology @belafrohn.bsky.social
May 21, 2025 at 8:35 AM
Can we build synthetic cells from de novo designed proteins?
Find out more in the latest review @natrevbioeng.nature.com from Bela Frohn, Shunshi Kohyama and Petra Schwille.
❕Publication: doi.org/10.1038/s442...
#ProteinDesign #SyntheticBiology @belafrohn.bsky.social
Find out more in the latest review @natrevbioeng.nature.com from Bela Frohn, Shunshi Kohyama and Petra Schwille.
❕Publication: doi.org/10.1038/s442...
#ProteinDesign #SyntheticBiology @belafrohn.bsky.social
Reposted by Philipp Becker
Protein design and optimization for synthetic cells
Protein design and optimization for synthetic cells
Nature Reviews Bioengineering, Published online: 19 May 2025; doi:10.1038/s44222-025-00318-1Bottom-up synthetic biology might greatly benefit from custom-made proteins as components of new biological systems. This Review discusses various protein optimization and design approaches, and explores how these can contribute to the generation of controllable synthetic cells.
www.nature.com
May 20, 2025 at 1:23 AM
Protein design and optimization for synthetic cells
Reposted by Philipp Becker
New Review out!
Can we eventually design not only proteins, but entire cells from scratch? Check out the review I wrote in @natrevbioeng.nature.com about how to combine protein design with synthetic cell science.
Link: www.nature.com/articles/s44...
Can we eventually design not only proteins, but entire cells from scratch? Check out the review I wrote in @natrevbioeng.nature.com about how to combine protein design with synthetic cell science.
Link: www.nature.com/articles/s44...
May 20, 2025 at 2:15 PM
New Review out!
Can we eventually design not only proteins, but entire cells from scratch? Check out the review I wrote in @natrevbioeng.nature.com about how to combine protein design with synthetic cell science.
Link: www.nature.com/articles/s44...
Can we eventually design not only proteins, but entire cells from scratch? Check out the review I wrote in @natrevbioeng.nature.com about how to combine protein design with synthetic cell science.
Link: www.nature.com/articles/s44...
Reposted by Philipp Becker
Reading group tomorrow: @json_yim and @woodyahern present "Atom level enzyme active site scaffolding using RFdiffusion2" www.biorxiv.org/content/10.1...
Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
May 11, 2025 at 5:11 PM
Reading group tomorrow: @json_yim and @woodyahern present "Atom level enzyme active site scaffolding using RFdiffusion2" www.biorxiv.org/content/10.1...
Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...
Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...