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Benedict Wolf

@bene837.bsky.social
51 followers 110 following 0 posts

PhD Student @ Niopek Lab - Uni Heidelberg Machine Learning for Protein Design

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Reposted by Benedict Wolf
Nicholas Southern @neuroscinikolai.bsky.social · 15/04/2026
1/28 How do you optimize a dynamic protein property that emerges from multiple states? Our finally published paper in @NatureComms takes on one of the hardest problems in protein engineering with phage assisted evolution: evolving allosteric switches🧵
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Jan Mathony @jmathony.bsky.social · 12/02/2026
🎉🎉 Our paper on temperature-dependent protein control using AsLOV2 variants is now published at @natchembio.nature.com: www.nature.com/articles/s41... including some new insights from extend variant characterizations.
nature.com
Modular engineering of thermoresponsive allosteric proteins - Nature Chemical Biology
Thermogenetics enables spatiotemporal control of protein activity using temperature. Now, engineering of a compact, insertable thermoresponsive protein module diversifies the classes of proteins amena...
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Martin Pacesa @martinpacesa.bsky.social · 27/08/2025
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...
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Nature Methods @natmethods.nature.com · 04/08/2025
Work by @bene837.bsky.social @jmathony.bsky.social @dominikniopek.bsky.social @uniheidelberg.bsky.social
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Reposted by Benedict Wolf
Nicholas Southern @neuroscinikolai.bsky.social · 13/06/2025
Excited to share my main PhD work is finally out! 🥳 We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)! See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞
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Dominik Niopek @dominikniopek.bsky.social · 05/05/2025
www.biorxiv.org/content/10.1...
biorxiv.org
Modular Engineering of Thermo-Responsive Allosteric Proteins
Thermogenetics enables non-invasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membra...
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Reposted by Benedict Wolf
Jan Mathony @jmathony.bsky.social · 01/04/2025
We have an exciting new PhD opportunity! If you are fsacinated by proteins and their dynamics and want to engineer them to develop new molecular tools: apply now! We are a young and dynamic team combining state-of-the-art laboratory and bioinformatics approaches. Please share.
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Reposted by Benedict Wolf
Michael Jendrusch @mjendrusch.bsky.social · 06/02/2025
New protein ML preprint from my PhD project. We describe salad (sparse all-atom denoising), a family of efficient protein structure diffusion models and show that it works well on a bunch of protein design task previously described in the literature. Preprint: www.biorxiv.org/content/10.1... (1/N)
Five generated protein structures coloured with a gradient from purple to teal. The structures are shaped and positioned to spell out the word "salad" – the name of the software described in the mentioned preprint – in all-capital letters.
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Reposted by Benedict Wolf
Arne Schneuing @rne.bsky.social · 15/01/2025
Our paper on computational design of chemically induced protein interactions is out in @natureportfolio.bsky.social. Big thanks to all co-authors, especially Anthony Marchand, Stephen Buckley and Bruno Correia! t.co/vtYlhi8aQm
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Niopek Lab @niopeklab.bsky.social · 16/12/2024
Excited to announce our optogenetic transcriptional deactivation toolbox is now out in its final form at Nucleic Acids research: academic.oup.com/nar/advance-....
academic.oup.com
A modular toolbox for the optogenetic deactivation of transcription
Abstract. Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high
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Niopek Lab @niopeklab.bsky.social · 05/12/2024
We are thrilled to share ProDomino a model for the prediction of domain insertion sites in proteins. Our approach enables the simple and rapid engineering of highly potent switchable proteins, as we exemplify by creating novel inducible variants of Cas9 and Cas12a. www.biorxiv.org/content/10.1...
biorxiv.org
Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites
Domain insertion engineering is a powerful approach to juxtapose otherwise separate biological functions, resulting in proteins with new-to-nature activities. A prominent example are switchable protei...
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Reposted by Benedict Wolf
Nicholas Southern @neuroscinikolai.bsky.social · 26/11/2024
Interested in regulating CRISPR-Cas systems for your experiments? Go check out these awesome chemical and optogenetic tools from our lab 👇 (made by some pretty cool people 😄)
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Reposted by Benedict Wolf
Jan Mathony @jmathony.bsky.social · 22/11/2024
Our paper on DMS of anti-CRISPR proteins is out in it's final form Nucleic Acids Research! Many congrats to first authors Tobias and Michael! It was lots of fun to see the story develop. academic.oup.com/nar/advance-...
academic.oup.com
A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins
Abstract. Deep mutational scanning is a powerful method for exploring the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins,
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