Simon Duerr @simonduerr Twitter profile

Last Seen Profiles

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@bokeplokalmalam

Simon Duerr

@simonduerr

3 years

I have created Bioicons - a library of 1632+ free, high quality science illustrations in vector format easily searchable and filterable specifically for the life science community. All icons are under permissive CC0 or CC BY license. ➡️

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Simon Duerr

@simonduerr

2 years

Redesign a protein in under 1 minute and verify the new sequence with AlphaFold using the improved ProteinMPNN app 1/3

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Simon Duerr

@simonduerr

2 years

Colab notebooks are great to share demos for bio or chemistry tools but it is hard to find them and they break easily so @kmjablonka and I built an aggregator website powered by Github Actions 1/

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Simon Duerr

@simonduerr

2 years

DiffDock is now on @huggingface Spaces with interactive visualization of the diffusion steps. Built using @Gradio and 3dmol.js and you can upload your own ligands as SMILES or sdf/mol2. Happy docking! 1/2

Gabriele Corso

@GabriCorso

2 years

Excited to share DiffDock, new non-Euclidean diffusion for molecular docking! In PDBBind, standard benchmark, DiffDock outperforms by a huge margin (38% vs 23%) the previous state-of-the-art methods that were based on expensive search! A thread! 👇

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Simon Duerr

@simonduerr

2 years

Introducing GradioFold - run protGPT2 and AlphaFold2 with just two button clicks to make de novo proteins in your browser. Built using @gradio 1/4

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Simon Duerr

@simonduerr

2 years

ProteinMPNN @huggingface now lets you predict all sequences in one go with AlphaFold2 and sort them by RMSD, score or pLDDT to pick interesting ones. For now you can run 15 seqs per run. 1/2

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Simon Duerr

@simonduerr

3 years

Sneak peek at the upcoming Bioicons @inkscape clipart extension. Simply search for illustrations directly within Inkscape (some other providers WikiCommons, Reactome are also available). A fresh batch of icons is also coming soon. #creativecommons #scicomm

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Simon Duerr

@simonduerr

6 months

In order to further the development of an open database of scientific illustrations for the life sciences we have now set up a non-profit under the umbrella of @OC_Europe 1/

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Simon Duerr

@simonduerr

2 years

ProteinMPNN + ESMFold now available on @huggingface Spaces. Any monomeric protein < 400 aa can be redesigned instantly and structures are predicted immediately using ESMFold API. 1/3

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Simon Duerr

@simonduerr

4 months

We investigated AlphaFold3 against RoseTTAfold-AllAtom and a new variant of Metal3D for prediction of metal-protein complexes. Tl;dr AlphaFold3 is as good as specialized tools on metal ion prediction. RFAA not so much. Some interesting findings in below thread: 1/

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Simon Duerr

@simonduerr

2 years

Short tutorial on how to visualize proteins on @huggingface spaces using @Gradio with 3dmol.js

Visualize proteins on Hugging Face Spaces

huggingface.co

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Simon Duerr

@simonduerr

1 year

Two years ago BioIcons was launched and the database has grown by almost 800 icons thanks to many scientists contributing illustrations ☺️ Now we're looking to grow more and need your feedback and support... 1/2

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Simon Duerr

@simonduerr

5 years

I quickly put together a @matplotlib version of this using @RDKit_org . Simply enter a SMILES string and your values as list and position the pie chart :) Prints out an SVG which you can edit in Inkscape or Illustrator.

Narayan Lab @ UMich

@NarayanLab

5 years

@nathandao1109 Thanks! We like to use this type of figure to concisely illustrate substrate scope. Figure guru @ScienceBey was the person in the group to pioneer this type of figure and it has spread like wildfire🔥

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Simon Duerr

@simonduerr

1 year

Use RoseTTAfold2 directly from PyMol with this @gradio demo: Interoperability is a key aspect of FAIR code. Glad that @Gradio makes it a piece of cake to build demos that can be interfaced with other programs via an API. 1/2

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Simon Duerr

@simonduerr

5 years

New version of the automatic radial scope plot, now with easier setup, automated positioning of the plots, organic substituents etc. Thanks to @dr_greg_landrum for the idea on how to automatically position the pie charts. cc @NarayanLab @ScienceBey

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Simon Duerr

@simonduerr

2 years

Novozymes is currently running a competition for single mutation Tm predictions - 25k $ prize money

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Simon Duerr

@simonduerr

2 years

Happy to present our new preprint on a deep-learning based method for rapid localization of transition metal ions in protein structures: Metal3D. Work done with @andrea_levy and @lcbc_epfl 1/6

bioRxiv

@biorxivpreprint

2 years

Accurate prediction of transition metal ion location via deep learning #bioRxiv

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Simon Duerr

@simonduerr

5 months

Many researchers including myself assumed that a @biorender publication license meant one could publish in any kind of journal including open access journals. However, the academic license forbids publishing CC BY implicitly. So how many papers are affected? 1/

Will Ratcliff

@wc_ratcliff

6 months

Time to ditch @BioRender ? I had no idea they were claiming copyright to the figures we make with it, even after we pay for use of the service.

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Simon Duerr

@simonduerr

2 years

You can now use Bioicons (and other free science illustration libraries such as @reactome ) directly from within Inkscape 1.2 if you click on File ➡️ Import Web Image ➡️ Select Bioicons in Dropdown. 🥳🥳 1/2

Inkscape

@inkscape

2 years

3-2-1... Launch! #Inkscape 1.2 is live! Head here for the details and to see the launch video: #colalboration #FOSS

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Simon Duerr

@simonduerr

2 years

New feature for proteinMPNN @huggingface - Positions can now be fixed with simple selection language such as "within 5 of resname ZN" or "within 6 of nucleic" to generate diverse sequences for enzymes or ligand binding proteins. 1/2

ProteinMPNN - a Hugging Face Space by simonduerr

huggingface.co

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Simon Duerr

@simonduerr

1 year

Protpardelle 🍝 is also available on @huggingface as webapp with interactive selection of the parts of a protein to redesign for conditional mode. 1/2

Alex Chu

@alexechu_

1 year

Code for Protpardelle is up now! sorry for the delay 😅 contributions and discussions welcome

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Simon Duerr

@simonduerr

5 months

New @gradio custom component for 2D molecule input using Smiles strings. Molecules can be input as strings or drawn using Ketcher. Demo and install instructions here 1/2

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Simon Duerr

@simonduerr

4 years

Let's have more virtual conferences even after travel restrictions are lifted. They are good for the environment and work-life balance. In order to help, I am designing a web platform that facilitates setting up a virtual meeting with a virtual poster session. 1/6

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Simon Duerr

@simonduerr

2 years

@datentaeterin @SZ @hmdeutschland @Zalando @aboutyou_com I think you'll enjoy this article where they show that all kinds of daily life items are subject to sexist design. They inverted the design of a mixer and a drill

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Simon Duerr

@simonduerr

7 months

First beta release of a native Molecule viewer for Gradio built on 3dmol.js: Gradio Molecule3D Simply install it using pip install gradio_molecule3d 1/3

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Simon Duerr

@simonduerr

3 years

If you use a webkit browser you can directly copy the icons as SVG into the clipboard and paste them directly in Illustrator and change colors, delete parts you don't want etc 🔥 (In Inkscape you currently get an image, but support for svg pasting is coming soon)

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Simon Duerr

@simonduerr

2 years

Awesome new feature that allows you run ProteinMPNN, DiffDock or Metal3D with one command on your own infrastructure.

Hugging Face

@huggingface

2 years

THIS IS BIG! 👀 It's now possible to take any of the >30,000 ML apps from Spaces and run them locally (or on your own infrastructure) with the new "Run with @Docker " feature. 🔥🐳 See an app you like? Run it yourself in just 2 clicks🤯

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Simon Duerr

@simonduerr

2 years

In addition to *fold, there are lots of structure➡️sequence models out there for "inverse folding". @ginaelnesr and I tried to collect them here: Let us know if we missed any!

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Simon Duerr

@simonduerr

10 months

Interesting new method for metal protein docking using a U-Net to predict a distance matrix of where the metal binds. Here is an unsolicited peer review of this work: (Also posted on BioRxiv Comments awaiting moderation)

bioRxiv Bioinfo

@biorxiv_bioinfo

10 months

DisDock: A Deep Learning Method for Metal Ion-Protein Redocking #biorxiv_bioinfo

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Simon Duerr

@simonduerr

2 years

Excited to talk about how to make protein ML models more accessible via publicly hosted demos. I'll speak about @Gradio @huggingface @streamlit @GoogleColab

Machine learning for protein engineering seminar

@ml4proteins

2 years

This week, we'll be having an interactive workshop with @simonduerr on Tuesday (3/28) @ 4 pm EST! Simon will give an overview + live demos on tools to publish and deploy models (like AF2, ProteinMPNN etc.) as web apps. See more at:

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Simon Duerr

@simonduerr

1 year

Glad that our work ( @_andrealevy @lcbc_epfl ) on Zinc ion site prediction is now published in @NatureComms More details in the preprint thread

Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins

Nature Communications - Zinc is an essential metal for many proteins. Here, the authors propose a model based on 3D convolutional networks to predict the location of zinc in experimental and...

www.nature.com

Simon Duerr

@simonduerr

2 years

Happy to present our new preprint on a deep-learning based method for rapid localization of transition metal ions in protein structures: Metal3D. Work done with @andrea_levy and @lcbc_epfl 1/6

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Simon Duerr

@simonduerr

5 months

Looks like there'll be no open code for AlphaFold3. At least, there is a server with 10 jobs per day and a server UI that looks pretty much like the @Gradio custom component I built for RoseTTAfold-AllAtom #opensource

RFAA - a Hugging Face Space by simonduerr

huggingface.co

Google DeepMind

@GoogleDeepMind

5 months

We have also launched AlphaFold Server, a free platform that scientists around the world can use for non-commercial research. 🔬 They can harness AlphaFold 3’s predictions and test hypotheses with just a few clicks - no matter their technical expertise. →

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Simon Duerr

@simonduerr

6 months

It's nice to see people questioning BioRender. While they do not claim copyright over the complete figures, scientists never own the figures fully if they use any of the icons therefore publishing the figures in open access journals under CC BY isn't possible! 1/

Will Ratcliff

@wc_ratcliff

6 months

Time to ditch @BioRender ? I had no idea they were claiming copyright to the figures we make with it, even after we pay for use of the service.

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Simon Duerr

@simonduerr

2 years

So many cool Google Colab demos these days on Twitter in the chemistry/protein space. Twitter search is pretty bad to find these again after some time. I wonder if the community should provide a space to collect links to all these demos for further inspiration. 1/2

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Simon Duerr

@simonduerr

3 years

Now I need your help: Found any bugs or other suggestions? More icons to add? Simply open an issue

GitHub - duerrsimon/bioicons: A library of free open source icons for science illustrations in...

A library of free open source icons for science illustrations in biology and chemistry - duerrsimon/bioicons

github.com

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Simon Duerr

@simonduerr

2 years

Here is a webapp that does not require installation for proteinMPNN (you can even try it from your phone) 1/2

ProteinMPNN - a Hugging Face Space by simonduerr

huggingface.co

Justas Dauparas

@JustasDauparas

2 years

1/5 Robust deep learning based protein sequence design using ProteinMPNN The high rate of experimental success and applicability to almost any protein sequence design problem has made it the standard approach at the @UWproteindesign

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Simon Duerr

@simonduerr

2 years

Results for this competition are online since a few days. Interesting that the very good intermediate results (Rs=0.8+) were mainly due to people overfitting to the public test data 🥸. Final winner achieved Rs ~0.55 for the private test data. 1/2

Simon Duerr

@simonduerr

2 years

Novozymes is currently running a competition for single mutation Tm predictions - 25k $ prize money

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Simon Duerr

@simonduerr

6 months

Arguably the easiest way of getting published in @Nature : Publish illustrations on for other researchers to reuse them. 1/2

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Simon Duerr

@simonduerr

4 years

Looking to organize a virtual conference with Poster session?. Try the beta version of my Virtual Conference Management System (VCMS) here First release will be soon, after weeding out some further bugs. List of features ⬇️

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Simon Duerr

@simonduerr

2 years

Over 120 new illustrations on Bioicons contributed by @MargotRiggi , @EmLedd1 , @SIB_SwissProt , @ferruz_noelia , Kathryn Kananen, Plant illustrations .... Happy to accept new contributions or icon requests at

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Simon Duerr

@simonduerr

3 years

Need an icon for your favorite type of vaccine? Or perhaps an NMR spectrometer? Or for your next cool advance in protein ML modeling? If you want to contribute your own illustrations simply fork the repo and submit a pull request as described in the Readme

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Simon Duerr

@simonduerr

2 years

Scrolling through the hilarious "I don't like jupyter notebooks talk" by @joelgrus - found this "But imagine" slide and looks looks like a pretty good description of what @Gradio does (except for 2)

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Simon Duerr

@simonduerr

1 year

For #30DaysOfGradio some pointers on visualizing proteins and molecules in your Gradio demos using 3dmol.js, Mol* and Smilesdrawer 1/

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Simon Duerr

@simonduerr

6 months

@baym @wc_ratcliff @BioRender @cshperspectives I have explicit confirmation from Biorender that CC BY was not okay without explicit written permission obtained by writing to a specific non public email address. As of November 2023 no CC BY at all possible anymore.

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Simon Duerr

@simonduerr

4 months

Interesting complement to our analysis on AF3 for protein-metal interactions. While for metals local context is used (e.g for His->Ala mutations), for other organic ligands like ATP AF3 does ignore local context of the pocket (e.g mutating all pocket residues to Phe).

bioRxiv

@biorxivpreprint

4 months

Do Deep Learning Models for Co-Folding Learn the Physics of Protein-Ligand Interactions? #bioRxiv

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Simon Duerr

@simonduerr

11 months

Now also available as vector art on under Creative Commons 0 license. Thanks @sasha_sundstrom You also are as talented as Sasha and have illustrations to share with the community? Submit them on

Dr. Sasha Sundstrom

@sasha_sundstrom

11 months

I drew some instruments for a presentation and then decided you should ALL have these. You can have these as nice clean TIFF files (also pasted into a PPT). Please enjoy and use for whatever! #RealTimeChem #ChemTwitter

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Simon Duerr

@simonduerr

4 months

You can find some more findings and a detailed performance comparison also against our more specialized model AllMetal3D in our preprint: 7/7

Predicting metal-protein interactions using cofolding methods: Status quo

Metals play important roles for enzyme function and many therapeutically relevant proteins. Despite the fact that the first drugs developed via computer aided drug design were metalloprotein inhibi...

www.biorxiv.org

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Simon Duerr

@simonduerr

6 months

Specifying the input for cofolding models just got easier with my new gradio component "gradio_cofoldinginput". Try it here to generate inputs for RoseTTAfold2 All Atom predictions including covalent modifications:

RFAA - a Hugging Face Space by simonduerr

huggingface.co

Rohith Krishna

@r_krishna3

7 months

Our work on modeling and designing biomolecular assemblies is now in @ScienceMagazine . RFAA Code: RFdiffusionAA Code:

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Simon Duerr

@simonduerr

2 years

@clathrin With latest inkscape you can now even directly search for bioicons within Inkscape . File➡️Import Web Image ➡️ Bioicons

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Simon Duerr

@simonduerr

2 years

@Dani_M_Stevens Very cool! Do you know about ? 1700 vector illustrations to kick-start Inkscape figures with some quality illustrations. I wanted to redraw a figure from a paper using Inkscape+BioIcons and record it for YT. Happy to contribute it to your platform.

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Simon Duerr

@simonduerr

2 years

Both the best and worst thing about doing a PhD: Interesting sideprojects

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Simon Duerr

@simonduerr

5 years

If you work with Jupyter Notebooks I recommend you to ditch the web interface and switch to VSCode. Such a nice experience with proper code completion and configurable theming.

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Simon Duerr

@simonduerr

5 years

A tragedy in two acts. I have just one question: Why? #compchem #reproducibility

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Simon Duerr

@simonduerr

1 year

2D Molecule editor with Gradio using Ketcher as Editor

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Simon Duerr

@simonduerr

5 years

Interested in QM/MM? There is a live stream of the @cecamEvents school on QM/MM methods in CP2K and CPMD until friday. Programm see: #compchem

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Simon Duerr

@simonduerr

1 year

Soluble weights now also on for you to play with directly in the browser. 1/2

Martin Pacesa

@MartinPacesa

1 year

We tried to solubilize the claudin, rhomboid, and GPCR membrane folds. Using vanilla ProteinMPNN, we were not able to design soluble versions of these proteins, so @JustasDauparas trained a new version called SolubleMPNN resulted in many soluble designs of these folds.

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Simon Duerr

@simonduerr

3 years

The site also has dark mode if you want to design with dark backgrounds and preview the icons with a darker background.

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Simon Duerr

@simonduerr

2 months

A good reminder to never only make available research code on GitHub but to keep an archived copy for releases on Zenodo. It's just a few quick and easy steps:

Referencing and citing content - GitHub Docs

docs.github.com

Marcelo D. Polêto - @mdpoleto.bsky.social

@mdpoleto

2 months

Not so fun news. @github made an unilateral decision to block not only the Making-it-Rain repo but they also blocked the entire account of our main dev @pablitoarantes without any explanation. Any explanation, @github ?

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Simon Duerr

@simonduerr

5 months

Pretty cool consequence of AF3 using diffusion is that pLDDT is no longer just for C-alpha but for each atom. RFAA still uses C-alpha pLDDT. Should enable interesting applications for locally refining rotameric states of predictions.

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@simonduerr

2 years

@GeneCollector @drawbiomed Thanks for highlighting! Actually if you open a recent Inkscape version you can click on Import Web Image in the File menu and select BioIcons in the drop-down 😊

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Simon Duerr

@simonduerr

3 years

68 new icons now on - including new Cell culture and molecular modelling categories. Thanks @MarcelTisch for contributing! If you want to share your own creations please do get in touch.

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Simon Duerr

@simonduerr

2 years

Curious about the scientific background behind ProteinMPNN? Tune in to this talk 4pm EST/1pmPST/10pmCEST. While you wait for the talk you can play with the interactive demo on @huggingface :

ProteinMPNN - a Hugging Face Space by simonduerr

huggingface.co

Machine learning for protein engineering seminar

@ml4proteins

2 years

24 hours until @JustasDauparas 's talk on designing proteins with ProteinMPNN! Sign up here for updates and zoom links: DM day of if you need the link!

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Simon Duerr

@simonduerr

1 year

@AdrianoAguzzi Very true! Unfortunately good illustrations also take time and skill. I tried to get funding to make BioIcons bigger but so far no luck 😢

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Simon Duerr

@simonduerr

3 years

💡 Use to cite references on slides instead of Lastname et al., Journal, 2022. Works for any long DOI from a journal, BioRxiv, Zenodo or DataCite. #ux #AcademicChatter

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Simon Duerr

@simonduerr

2 years

The protein ML community needs this ⬇️

Ben Blaiszik

@BenBlaiszik

2 years

We will build Model Gardens; i.e., collections of curated models linked with data/computing resources needed to advance research communities. Gardens will include automated model software/hardware/task testing and uncertainty quantification.

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Simon Duerr

@simonduerr

2 years

Thanks to @sokrypton 's AF2 speed trick inference for 6MRR now takes mere 20 seconds right in your browser without install or any other waiting time. Thanks @huggingface / @Gradio for making this incredibly easy. 2/3

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Simon Duerr

@simonduerr

2 years

Added over 400 new illustrations from @togopic to bioicons (e.g LC-MS) Thank you/ありがとうございます @dbcls AND you can now more easily submit your own illustrations. 1/2

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Simon Duerr

@simonduerr

5 months

This is common pattern also for @NaturePortfolio . Some examples: I tried requesting data from a paper "available on reasonable request". When the authors didn't respond I contacted the journal as lined out in their open data guidelines. No response since last october! 3/

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Simon Duerr

@simonduerr

6 months

3/ Collectively, scientists spend probably 17.9 - 33.8 Mio $ per year on BioRender. I've pitched an idea for an open database to many different funders but so far no one has taken me up on it. With a tenth of BioRender revenue we could establish a forever free database. 4/4

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Simon Duerr

@simonduerr

3 years

Bioicons ❤️ @drawio / @inkscape - Two new extensions for Bioicons are now available: 1) -Go to , select the categories you need and launch the editor. Save locally or in the cloud and embed the drawings in your slides.

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Simon Duerr

@simonduerr

7 years

#Schafpostkarte vom Säntis @schafzwitschern

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Simon Duerr

@simonduerr

11 months

BioIcons has reached 1000 stars on github 🤩 The project is looking for new developers and submissions for new illustrations are always welcome on Reach out if you're interested in contributing.

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Simon Duerr

@simonduerr

2 years

Really glad to spend an extended summer in the Bay Area as a visiting researcher in Possu Huang's lab. Thanks @firmenich / @EPFL_ReO for financial support. 1/2

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Simon Duerr

@simonduerr

5 months

Bioicons has a blog now, here we'll share updates on the cause of FAIR scientific illustrations. First post is on licenses for illustrations: 1/

A short primer on licensing for illustrations

Illuminating the license jungle

blog.bioicons.com

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Simon Duerr

@simonduerr

6 months

@baym @DaniBeckman @dava_keavney @nquinoneso It's even worse. In an Open Access journal like Nature Comms you actually cannot use BioRender figures since Biorender doesn't allow you to publish the figures you created under CC BY even if you pay for them.

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Simon Duerr

@simonduerr

5 months

It's unlikely this paper even needed this kind of peer review since a test of time by the community would've evinced any shortcomings anyway. Nature clearly only cares about profit and reputation like all other big commercial publishers and not about open science. 2/

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Simon Duerr

@simonduerr

2 years

Props to the authors ( @GabriCorso @HannesStaerk et al.) that made the code available in contrast to most other papers for diffusion models in the bio space . Would love to add other models in the space as comparison. 2/2

GitHub - gcorso/DiffDock: Implementation of DiffDock: Diffusion Steps, Twists, and Turns for...

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking - gcorso/DiffDock

github.com

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Simon Duerr

@simonduerr

5 years

Microsoft has a cool Google scholar alternative ready. Looks neat and can open links to papers in new tabs (which is a constant annoyance for me when scrolling through Google scholar profiles)

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Simon Duerr

@simonduerr

11 months

Kudos to @PacBio for releasing illustrations of their devices on as high quality vector art under CC0 for scientists to reuse for illustrating lab protocols or scientific articles ! More device manufacturers should be doing this! Thx @jessemellon

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Simon Duerr

@simonduerr

4 years

PowerPoint has a pretty nifty presentation coach for rehearsing presentations. Tracks pace, voice pitch, originality and even highlights profane language. Already available on the web and apparently coming to Desktop soon. I'll be using this to rehearse for my next talk.

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Simon Duerr

@simonduerr

11 months

@sasha_sundstrom @ReidAlderson These are great ! I'm the developer of I'd be happy to vectorize them for you and put them on the platform if you let me know which license you want to use. Sounds like you would be okay with CC0, but CC BY with mandatory attribution also is a good choice

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Simon Duerr

@simonduerr

7 months

Looking for a biologist that knows the tree of life very well to help me categorize this nice collection of vector illustrations by @pjkeelinglab for 🧬

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Simon Duerr

@simonduerr

4 years

A lesson in why preprints are the better system that accelerates science and is less biased towards big (western) institutions/names.

ChemBark

@ChemBark

4 years

Virginijus Šikšnys has everyone beat as far as most gutting desk rejection of all time.

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Simon Duerr

@simonduerr

1 year

Please fill the BioIcons User Survey at and sign the Statement of Support. More Users/Supporters will make it will be easier to convince funding agencies to fund new illustrations. 2/2

BioIcons: Letter of Support

BioIcons is looking for funding to increase the size of its illustration catalog and provide new features on the website. Since this is platform for scientists from scientists, we need your opinion...

docs.google.com

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Simon Duerr

@simonduerr

4 years

Our Genetic Algorithm approach to predict protein thermostability for #AIchem20posters @RSC_CICAG . Explore the poster and some of the data interactively here: Preprint and next iteration using deep learning is in the works.

P07: EVOLVE

A Genetic Algorithm to predict Protein Thermostability

dev.simonduerr.eu

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Simon Duerr

@simonduerr

2 years

RCSB search/filtering capabilities are pretty nifty so it's cool that they integrated AFDB

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Simon Duerr

@simonduerr

6 months

@baym @wc_ratcliff @BioRender @cshperspectives I also sent them two example articles with Biorender figures under CC BY and they told me the articles will need to be corrected. When I sent them 9000 more articles they ghosted me...

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Simon Duerr

@simonduerr

4 years

Google @googlechrome has tab groups now. Very helpful to structure the myriad of open browser tabs I always seem to accumulate :/ . Activate using chrome://flags "Tab Group" -> Enable

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Simon Duerr

@simonduerr

6 months

@wc_ratcliff @BioRender After I complained last year they published this guide CC BY is not possible !

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Simon Duerr

@simonduerr

2 years

Making viral molecules, eh? @tiktok_us

Tejas K. Shah

@T_K_Shah

2 years

Uhh TikTok and Comp Chem? @Chemjobber

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Simon Duerr

@simonduerr

5 months

Also copyright violations: I sent @NaturePortfolio 6454 papers with likely copyright violations in open access papers in January, they thanked me for the email but they still continue to happily publish the exact same copyright violations 4/

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Simon Duerr

@simonduerr

4 years

@peter_simone @DerUCas @boelwtermine @Naturland_eV @bioland_de @demeter_de @AnthroBlogger Es waere schoen wenn die Gruenen auf Distanz zur antroposphischen Landwirschaft gehen wuerden und sich fuer effiziente nachhaltige Landwirtschaft einsetzen wuerden. Und nebenbei: Ein pauschales Nein zur Gentechnik in der Landwirtschaft ist unwissenschaftlich. 1/2

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Simon Duerr

@simonduerr

2 years

Want bigger proteins or multimeric ones? Clone the repo and run it locally or on colab with the same UI. You only need a somewhat beefy gpu with > 16GB RAM. Instructions for local install here: 2/3

README.md · simonduerr/ProteinMPNNESM at main

huggingface.co

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Simon Duerr

@simonduerr

5 years

@BWusstsein @Needie_ @Topfritte Diese Rate gibt es nur in einer Provinz und nur für die Erstimpfung. Für wirksamen Impfschutz und Herdenimmunität braucht man allerdings zwei Impfdosen.

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Simon Duerr

@simonduerr

2 years

Best academic conference swag so far: Themed socks @UniWarszawski 🧦🧦

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Simon Duerr

@simonduerr

4 years

@PaulRobustelli Might want to check out this resource with plenty of examples

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Simon Duerr

@simonduerr

2 years

@agrossfield @leslievosshall @HHMINEWS @ardemp There is a also

Simon Duerr

@simonduerr

3 years

💡 Use to cite references on slides instead of Lastname et al., Journal, 2022. Works for any long DOI from a journal, BioRxiv, Zenodo or DataCite. #ux #AcademicChatter

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Simon Duerr

@simonduerr

5 years

"93% of the papers published in the first ten months of 2019 in Nature Materials declare that at least some of the data are available only from authors upon request..." What an argument for banning this phrase from any serious publication.

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Simon Duerr

@simonduerr

2 years

P.S Interactive manuscript is powered by #manubot /pandoc (DOCX, TEX->PDF and web version all generated from the same source) and web app can be easily implemented via @huggingface / @gradio /3dmoljs. Happy to help/provide advice if you want to host your own interactive manuscript.

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Simon Duerr

@simonduerr

2 years

A beautiful example is the MID1 protein (PDB 3V1C). Keeping the zinc binding residues fixed, ProteinMPNN is able to generate diverse sequences that fold back into the 3D structure with RMSD ~2-3 Å 2/2

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