Assistant Professor UAS at HES-SO Valais-Wallis 🇨🇭 🤗 HF Fellow. Working on AI, Protein Design and Open Science. Creator of https://xitter.cf/t.co/Y9GsDuZ0L1

Lausanne
Joined July 2012
Simon Duerr retweeted
Some studies earlier this year found that MSA pairing quality has no impact on structure prediction of co-evolving hetero-oligomeric complexes. I'm curious if co-folding models trained with the MSA pairing approach by @yoakiyama would do better xitter.cf/BioSpace9/status/20442…
Dissecting the Black Box of AlphaFold in Protein-Protein Complex Assembly biorxiv.org/content/10.64898… この研究は、AlphaFoldがどのようにタンパク質複合体の構造を予測しているのかを理解することを目指しています。 特に、従来重要と考えられていた共進化情報ではなく、単体タンパク質の形状や界面の形の相補性が重要であるという視点で解析が行われています。 モデル内部の情報伝播を可視化することで、まず単体構造が決まり、その後に相互作用が推定されるという段階的な推論プロセスが示されています。 この理解は、protein designにおいて複合体を設計する際に、どの要素を重視すべきかを考える上で重要な示唆を与えます。
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Simon Duerr retweeted
Excited to report the first de novo enzyme catalyzing two of the most energetically demanding reactions in biology—phosphomonoester and phosphodiester hydrolysis—with catalytic efficiencies comparable to natural enzymes! 🚀 desB was designed zero-shot with dEVA. No structure prediction, no pre-defined motif, no reaction-intermediates. 🧵 @StanfordBiosci @bioe_stanford @SLAClab @EPFL @hes_so @simonduerr
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Simon Duerr retweeted
Today we're dropping the "beta" tag from Adaptyv, launching our new website and announcing our $8M seed round. When we started Adaptyv a few years ago, our core belief was: AI models for biology are only as good as the experimental data they're trained on and the hypotheses they can test in the real world. Now, after a year of working with many great partners, we’ve scaled our infrastructure to the point that we're now open to anyone who wants to use our platform! Overall, this year, over 30 companies started using Adaptyv to validate their protein designs - from some of the biggest pharmas to frontier AI labs to many, many techbio startups. We've run hundreds of experiments, tested well over 10,000 proteins this year and are generating the data that validates the best AI models currently in development.
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Simon Duerr retweeted
Chai Discovery just released their new model Chai-2, validated on Adaptyv! Chai-2 enables generation of de novo proteins and epitope-specific antibodies using a multimodal generative architecture that integrates all-atom structure prediction and generative modeling. Chai tested many of their new protein designs using our high-throughput wet lab at Adaptyv to get high quality data to improve their AI models in as little as two weeks per round.
We’re excited to introduce Chai-2, a major breakthrough in molecular design. Chai-2 enables zero-shot antibody discovery in a 24-well plate, exceeding previous SOTA by >100x. Thread👇
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Thank you to everyone who came to MLSB this year!! We are collecting feedback in a short 2 minute survey (and more data means maybe next year we'll train a new model... or just get a bigger room 😄) forms.gle/WHFNfvxVh3QxuTXZA
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Open-access journals publish content under the CC-BY copyright licence, which means that anyone can copy, distribute or transmit that work as long as the original creator is credited. But the inclusion of BioRender illustrations complicates the matter. chemistryworld.com/news/thou…
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Our submission portal on CMT is live! 👀 Deadline to submit is Sep 18 11:59pm AoE. See mlsb.io for call for papers and more info. And, mlsb.io/#challenge now hosts a P/L/INDER leaderboard! Show us your models!
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Simon Duerr retweeted
Truly sad that three months after promising to do better @BioRender is still interfering with both publication and preprinting
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The Machine Learning in Structural Biology workshop will be back at #NeurIPS for its 5th edition in December! Stay tuned as we will soon share details about the stellar lineup of speakers 🌟, the call for papers 🧬, and a very exciting innovation for this year's workshop 🥁🚀!!
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*Of course* journals should publish work from the private sector — which indeed invests more in biomedical research than the public sector — but not with a separate set of criteria. Also IMO editorials should be signed. As those at journals well know, authorship isn’t just about credit, but also about responsibility Nature’s response to publishing AF3 w/o the code: nature.com/articles/d41586-0…
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Announcing AlphaFold 3: our state-of-the-art AI model for predicting the structure and interactions of all life’s molecules. 🧬 Here’s how we built it with @IsomorphicLabs and what it means for biology. 🧵 dpmd.ai/3URDiNo
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Webpage's live: ml4lms.bio Update's there to follow!
Our workshop ML4LMS = "ML for Life and Material Science: From Theory to Industry Applications" has been accepted for ICML this year. We have a fantastic line-up and are quickly editing submission guidlines, a website, and much more.
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Simon Duerr retweeted
Chenxin Li, PhD (@chenxinli2.bsky.social)@ChenxinLi228 Feb 2024
Just contributed another vector art to bioicons. A free library of high quality science illustrations under permissive license bioicons.com by @simonduerr If you make your own vector arts for papers/presentations, consider contributing them to bioicons.
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A one-click blog: all icon libraries, resources and tools for making a great #GraphicalAbstract - feel free to read/comment/share (and stay tuned for part 2, colors and layout!) helenajamborwrites.netlify.a… #ScienceVisualizations #scicomm #Academic #dataviz #SciViz #ScienceFigures
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Simon Duerr retweeted
Chenxin Li, PhD (@chenxinli2.bsky.social)@ChenxinLi212 Nov 2023
I added “contribute vector art icons to Bioicons.com” to the volunteering section of my CV. If you have original vector art icons that you feel proud of, please consider contributing to Bioicons.
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We are happy to announce the first @LogConference Meetup in Lausanne, supported by @vant_ai! 🤗 Join us on Nov 22nd at @EPFL_en to hear @_bunnech, @ClementVignac, @DorinaThanou and @m_deff. Bring your posters! Registration: forms.gle/c4HjeuDoBTpXN95F9 Webpage: sites.google.com/view/log-me…
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I'm so excited to share with you all what the Gradio team has been working on for the past few months 🤗 Join us in the 4.0 launch livestream tomorrow (Tues. Oct. 31st) at 9 AM PST (so like 22 hrs from now) youtube.com/watch?v=5MgmKBCO…
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Imaging Lunch on November 1: Creating scientific illustrations with BioIcons and BioRender with @simonduerr in collaboration with @EPFLOpenScience. Details & registration: memento.epfl.ch/event/imagin…
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It was great to teach about protein design (PyRosetta, ProteinMPNN, RFDiffusion, AF2) at the FEBS advanced course "Computational Approaches to Understanding and Engineering Enzyme Catalysis" in beautiful Zagreb. computationalenzymeengineeri… Want to try out the notebooks?
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