thecodingbiologist

Creating tools and tutorials to make lab life a little easier.

[Ben Fry @benf549]

My first-author paper describing our protocol for the zero-shot de novo design of drug-binding proteins is now available as an article in Nature! Here’s what we did and what's new from the preprint posted last year 🧵 (1/10):

[Kresten Lindorff-Larsen @LindorffLarsen]

Everything you wanted to know about the protein chemistry behind how amino-acid changes affect the cellular abundance of proteins

Effects of residue substitutions on the cellular abundance of proteins
https://t.co/FwoD1kiF30

[Tycho Mevissen @TychoMevissen]

Excited that our work on transcription-coupled DNA repair is now published @CellCellPress! We recapitulated TC-NER in Xenopus egg extract and identified STK19 as a core repair factor that couples stalled Pol II to TFIIH. 🧬🐸

➡️ https://t.co/0SDr81nzhu

[Ernst Schmid @ernstschmidd]

Make publication ready figures from your #AlphaFold PAE files. Works on multimer and AlphaFold 3 files. Customize colors and export as an SVG for editing in illustrator! https://t.co/6aFwXRqOKs

[Ernst Schmid @ernstschmidd]

Excited to share that our new preprint is out! We used #AlphaFold multimer to screen 7000+ nuclear proteins to find new nucleosome acidic patch binders. Great collaboration between @FrogWalterLab and @LucasFarnung. https://t.co/CScq14Ssgw

[Ernst Schmid @ernstschmidd]

Riding the #AlphaFold3 wave with a new analysis tool. It’s super new/unpolished, but would love to get community feedback! Extract and filter residue level interaction data from your AF3 server prediction zip files! Try it here: https://t.co/PGy6IwRdk3

[Peter Mullen @PeteMullen]

So excited to share the first work from our lab. Led by @StevePilley with help from lots of amazing collaborators. A special shout out to @LyssiotisLab and @BKennedy_aging and their labs!

[Yasha Ektefaie @YEktefaie]

Introducing the SPECTRA python package!

https://t.co/a1dKDRmtGo

This package implements the spectral framework for model evaluation. All you need to get started is (1) a model, (2) a dataset, and (3) a definition of sample to sample similarity!

[Grant Sanderson @3blue1brown]

I just posted the first of what will be several chapters about transformers, which in the last year has been the most requested topic for the channel.

https://t.co/j1LMXSor6c

[Bo Wang @BoWang87]

couldn’t agree more about the need for more computational biologists. More importantly, we must ensure they receive the recognition and support they deserve. Their work should never be dismissed as merely “just service”. Additionally, I’d like to remind everyone of the excellent paper titled ‘All Biology is Computational Biology’. 🧬 💻

[Gygi Lab @GygiLab]

Check out this massive study led by @GygiLab member Jonathan Van Vranken and lab alumnus @dschweppe1 to learn how thermal stability measurements and small molecule screening can be used together to tease apart the compounds' direct and indirect effects!

[Anne Carpenter, PhD @DrAnneCarpenter]

Our essay in Nat Cell Bio:
"Bringing computation to biology by bridging the last mile"
We argue to shift resources/rewards towards creating user-friendly software to bridge computation and biology-it yields huge returns!
@shantanuXsingh
Free author link: https://t.co/B0H1v29SBI

[thecodingbiologist @codingbiologist]

A higher power

[Johannes Hagemann @johannes_hage]

today I learned that there’s a literal GPU church with 4k H100s in Barcelona

h/t @tugot17

[thecodingbiologist @codingbiologist]

Stringz: A GUI based string manipulation tool https://t.co/C0gylXpMCa via @producthunt

[thecodingbiologist @codingbiologist]

Analyze strings, reveal hidden characters, visualize character indices and more:

https://t.co/VpD61oXfEb

[thecodingbiologist @codingbiologist]

Drop an #AlphaFold PDB file, select the chain and or region you want to analyze, and export the pLDDT values. It's that easy:
https://t.co/PTbzJQtNd8

[thecodingbiologist @codingbiologist]

Finally, export your edited plot as a PNG or SVG, and export the error scale along with it!

[thecodingbiologist @codingbiologist]

Wishing you could easily edit your #AlphaFold PAE plots to make publication quality figures? Try out my latest tool, a PAE viewer that allows you to easily upload, edit, and export high quality plots. https://t.co/UTpyZSLPAt.

[thecodingbiologist @codingbiologist]

Next, edit colors, lines, names, detect and label chains.