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Simon Duerr Profile
Simon Duerr

@simonduerr

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

Lausanne
Joined July 2012
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@simonduerr
Simon Duerr
11 days
RT @adaptyvbio: Chai Discovery just released their new model Chai-2, validated on Adaptyv! . Chai-2 enables generation of de novo proteins….
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@simonduerr
Simon Duerr
5 months
In earlier work, we already analyzed how AllMetal3D given a structural input and no information about metal stoichiometry fares against co-folding methods given metal stoichiometry but no structure:
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@simonduerr
Simon Duerr
5 months
We compared to a few other tools that perform either metal identity prediction or location prediction and found that is very important to include negative classes during training and also cluster metal ions by biological similarity.
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@simonduerr
Simon Duerr
5 months
We've made available a ChimeraX extension and a Webapp to easily run predictions. AllMetal3D is now also easily installable using pip. ChimeraX: HuggingFace: Docs for Python Package:
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@simonduerr
Simon Duerr
5 months
Excited to share our new AllMetal3D model building on Metal3D. AllMetal3D predicts the location, identity and geometry of the major biologically relevant metal ions
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@simonduerr
Simon Duerr
7 months
RT @workshopmlsb: Thank you to everyone who came to MLSB this year!! . We are collecting feedback in a short 2 minute survey (and more da….
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@simonduerr
Simon Duerr
8 months
Anyone working at MPG willing to share the license conditions ? I'd be curious if they have special terms. For the last contract they didn't. The info should be on this page:
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@simonduerr
Simon Duerr
8 months
Unbelievable how expensive BioRender is. @MPDL is paying 673 413 USD for a two year license for a software that isn't even compatible with open access publishing (even if BioRender claims otherwise).
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@simonduerr
Simon Duerr
8 months
Note that this is an Alpha release. It will soon be also possible to define modified residues, covalent modifications and view confidence. Ping me if you encounter problems.
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@simonduerr
Simon Duerr
8 months
Both the input component and the molecule output component are individually reusable. Simply pip install gradio_cofoldinginput or gradio_molecule3d.
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@simonduerr
Simon Duerr
8 months
This is a portable interface. You can easily run in on your local infrastructure using Docker. There is also a REST API interface.
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@simonduerr
Simon Duerr
8 months
Now available: open source UI with @Gradio for Boltz-1 by @GabriCorso @jeremyWohlwend .Check it out on HuggingFace spaces. h/t @huggingface for community L4 GPU:
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@GabriCorso
Gabriele Corso
8 months
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with @jeremyWohlwend, @pas_saro and an amazing team at MIT and Genesis Therapeutics. A thread!
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@simonduerr
Simon Duerr
8 months
All platforms that forbid commercial use like BioRender or BioGDP are simply incompatible with Open Access publishing under CC BY even if they claim otherwise. Your CC BY published paper will likely need a correction in the future to fix the copyright if you use e.g BioRender.
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@simonduerr
Simon Duerr
8 months
This is a great effort by NIH. All illustrations financed by public money should similarly be available for others to reuse in the correct format (vector). The key is that NIH BioArt is not only free but also comes with a permissive license! #OpenScience.
@NIAIDNews
NIAID News
8 months
📢NIH BioArt Source, a free new science and biomedical art resource library, offers a diverse array of high-quality illustrations, vectors, & brushes, free to use & download. See the full catalog of free science and #biomedical illustrations: #FreeResource
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@simonduerr
Simon Duerr
8 months
You can play with the demos directly in the slides thanks to @Slidevjs 😎.
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@simonduerr
Simon Duerr
8 months
Gave an intro to Docker + @huggingface Spaces + @Gradio at European Rosettacon 2024 for protein people. Maybe my slides are also interesting to the wider community:
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@simonduerr
Simon Duerr
8 months
And if you want to support BioIcons in funding applications and make your voice heard it is still appreciated if you fill the user survey and tell us what you need from open scientific icons:
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@simonduerr
Simon Duerr
8 months
Glad to share the first results from the ongoing user survey on BioIcons. Really appreciate that it's used around the globe! You can read more about the results here:
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@simonduerr
Simon Duerr
8 months
RT @ChemistryWorld: Open-access journals publish content under the CC-BY copyright licence, which means that anyone can copy, distribute or….
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@simonduerr
Simon Duerr
8 months
Typed up my thoughts on the BioGDP license here:
@simonduerr
Simon Duerr
8 months
Eventful week for visual science communication. just got published in NAR. The platform features a web editor and database with many icons (all free). Unfortunately, looking at their ToS I cannot recommend to use it.
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