Artem

This is the book that got me into biology! Nick Lane doesn't miss. Mitochondria, transformer and oxygen books are super as well.

You want to start tomography? Solve structures inside cells? Reach Nyquist 😳 ? @phaips.vd.st and I have a website for you! tomoguide.github.io
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !

Walked Assisi to Rome last summer. They don't leave you alone.

I hear you. My impression is that people are either too comfortable, too meek or just too busy. Most of the output is just a kind of moralizing indignation online. I'm referring to the academic community on bsky. Not sure what has to change short of worldwide cataclysmic science cuts.

why aren't you?

GitHub - martinpacesa/BindCraft: User friendly and accurate binder design pipeline User friendly and accurate binder design pipeline. Contribute to martinpacesa/BindCraft development by creating an account on GitHub.

New Title Alert: BindCraft- a user friendly and accurate binder design pipeline.

Learn more here: https://buff.ly/3CEqPpU

#SBGrid #SBGridSoftware #StructuralBiology

the twink will say whatever is convenient at this time of R1 fixation, which is open source, which makes OAI look incompetent

jealous, bro

Here's to successfully capitalizing on our socialist peeves and selling out.

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...

Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍

Preprint📜: www.biorxiv.org/content/10.1...

A short thread🧵👇

New imaging methods have produced lots of data about how cells are organized. But how to find the information that's out there? @marymirvis.bsky.social shows how in poster B567 Comparative cell anatomy through research synthesis of the whole-cell microscopy literature Mon Dec 16 11:15 - 12:45

I'm presenting a new paper "Exploring Discrete Flow Matching for 3D De Novo Molecule Generation" at @workshopmlsb.bsky.social this week! More info in this thread but reach out if want to chat at NeurIPS about generative models or molecular design. arxiv.org/abs/2411.16644

Adaptyv Bio hosted an antibody engineering competition to design/engineer binders to EGFR. Super stoked that we came in first place with the Cradle team! We’ll be talking about the methods used at #NeurIPS this coming week!
Here are the full results

foundry.adaptyvbio.com/competition

Fermat's Library | The Consequences of One’s First Programming Language annotated/explained version. Fermat's Library is a platform for illuminating academic papers.

"My observation is that, more important than one's first programming language is one's first substantial (i.e. 6 months to write) program. ...spent much of their remaining professional lives trying to repeat it, improve on it, or prove it is the best."
fermatslibrary.com/s/the-conseq...

Protein engineering at the next level: a framework for in silico mutational scanning and protein stability without the need in extensive training. It integrates evolutionary and structural insights to propose substitutions particularly for multi-state proteins onlinelibrary.wiley.com/doi/10.1002/...

Blog post link: diffusionflow.github.io/

Despite seeming similar, there is some confusion in the community about the exact connection between the two frameworks. We aim to clear up the confusion by showing how to convert one framework to another, for both training and sampling.

Years after the idea and preliminary experiments, Claire Coupland's amazing structure of the endogenous vacuolar- or vesicular-ATPase in its NATIVE vesicle is now in bioRxiv "High resolution cryo-EM of V-ATPase in native synaptic vesicles"
www.biorxiv.org/content/10.1...

Happy to share our new review on the structural pharmacology of TRP channels!
Check out the supplementary table, which includes a list of all ligands, corresponding PDBs of complexes with TRP channels, and reported affinity values.

www.sciencedirect.com/science/arti... #ionchannel #TRPchannel (1/5)

Does this thing work on linux machines? Haven't tried it yet seeing only mac/win binaries on their website.
Thanks for packaginng

Post a non-religious photo you think of as holy.
Not necessarily holy, just cool contrast between "then and now" in ribosome assembly landscape understanding. Nierhaus map from the 80s / AV Broeck & Sebastian Clinge in Science 2023.

Single-particle Cryo-EM and molecular dynamics simulations: A perfect match Knowledge of the structure and dynamics of biomolecules is key to understanding the mechanisms underlying their biological functions. Single-particle …

Our review paper on cryo-EM🤝MD simulations just appeared online! Thanks to Pilar Cossio and Edward Egelman for editing the cryo-EM themed issue of COSB! www.sciencedirect.com/science/arti...