Olive Laprévote 🌻

PhD student at Höcker Lab, trying hard to design protein walkers!
Hitchhiker 👍
Street juggler 🤹
He/she/they

[Niko McCarty. @NikoMcCarty]

We are really excited to finally share this resource. We hope it becomes a useful starting point for biology students. Please let us know if you have any feedback!

[💦 Dr. Alex Gener (he/él) @Cas9Bandit]

TINY. SHOES.

I repeat:

TINY

SHOES.

[Jorge Bravo Abad @bravo_abad]

A new resource for protein design: the Protein Design Archive

Protein designers have long aimed to explore the vast possibilities beyond nature’s existing structures, seeking to learn how amino acid sequences fold and function in ways that evolution never tested. Chronowska et al. unveil a new database and website known as the Protein Design Archive (PDA) that aggregates and curates experimentally validated protein designs from the past four decades. This resource highlights the astonishing progression from small, manually tweaked constructs to complex, computationally generated folds, providing a window into how de novo design can help address scientific and societal challenges.

The authors created the PDA by systematically scanning the Protein Data Bank (PDB) for synthetic sequences (taxonomy identifier 32630) and curating results to remove entries that were merely natural proteins with minor mutations. The database holds over 1,500 structures, each annotated with sequence-based and structure-based similarity metrics to provide insight into how these designs deviate from both one another and from known natural proteins. A user-friendly interface enables filtering by date of release, search terms, and novelty scores, while monthly updates ensure its data remain current. Throughout, the authors have balanced inclusivity (capturing a broad range of designs, including historic but unpublished examples) with rigorous hand-checking to maintain quality.

The researchers discovered that protein design efforts have accelerated dramatically, with a discernible shift around 2009–2010 when accessible computational tools like Rosetta further expanded de novo design’s reach. More recently, the advent of deep learning approaches has nearly tripled the annual output of new structures. The PDA not only showcases how designed proteins increasingly mirror the mass, complexity, and packing of their natural counterparts but also helps reveal persistent biases in secondary structure usage. By hosting a comprehensive, regularly updated collection, the archive empowers protein engineers to compare methods, pinpoint gaps, and pursue ambitious new directions that deepen our mastery of protein structure and function.

Paper: https://t.co/HoBLrARgeX
Website: https://t.co/MYakoZnhU8

[Patrick Bryant @Patrick18287926]

I'm hiring a new postdoc in protein design (wet lab) at Stockholm University/SciLifeLab. The work will focus on expanding our work on binder design and using new AI models that we are developing. Apply here: https://t.co/Y52eedbB0i

[Clockwork @this_clockwork]

🍂NEW VIDEO🍂
All through Autumn, trees race against time to recycle their chlorophyll--and basically everything else in their leaves.

But why go through all this effort?

The answers are honestly mind-blowing:

rendered in #blender3d using @bradyajohnston's #molecularnodes

[David S. Goodsell 🏳️‍🌈 @dsgoodsell]

I'm very happy to announce that I have retired! I'm equally happy that @janetiwasa has agreed to continue the Molecule of the Month @buildmodels. Read about this at https://t.co/fs5LBpfL9E

[Zion Lights @ziontree]

A picture speaks a thousand words.

Air pollution is deadly. Displacing fossil fuels with nuclear energy saves lives.

[Olive Laprévote 🌻 @PestoFasta]

@JeffreyRMillman Somewhat. Checking the PubPeer page (1) it appears the NSF tried it on freshly cut muscle tissues (2).
1: https://t.co/eeum2Kne3G
2: https://t.co/591DVuENId

[transmum @trans_mum]

Just here to say that puberty blockers and hormone therapy turned my suicidal daughter into a thriving teen and award winner. She’s thriving.
#ListenToTransYouth

[Ernesto Arias-Palomo @EAriasPalomo]

Our experience with #alphafold3 🤖 (code recently released) and some of our most recent #cryoEM 🔬 structures (thread below) https://t.co/SmX8i15Zwa
https://t.co/hwJUlkwhye

[Arthur Zalevsky @ArthurZalevsky]

What a week! First, @GoogleDeepMind fulfilled its #AlphaFold3 promise, and now @chaidiscovery delivered a long-awaited killer feature - custom distance restraints: https://t.co/LEPpdrM3fG! Here is a 7SYZ (AB-protein) example (x-ray in white).

[Blender 🔶 @Blender]

Blender Foundation and the online developer community are proud to present Blender 4.3! 🎉

Packed with exciting improvements to existing tools (hello EEVEE Light Linking and multi-pass compositing!), performance boosts, and the foundations for the future (looking at you, Grease Pencil v3).

Plus, hundreds of contributions ranging from new features to accessibility enhancements—and as always: loads of fixes.

Read the notes: https://t.co/zB1ew2VItT

#b3d #DevFund

[IOP Nano @IOPnano]

Walking by design: how to build artificial molecular motors made of proteins
In this beautiful article by @HeinerLinke et al @lunduniversity, the future design challenges and prospects of autonomous walking proteins are discussed.

Just Accepted:
https://t.co/aCbJtEr7bO

[Kresten Lindorff-Larsen @LindorffLarsen]

Looking forward to see 260 participants at the 10th annual Linderstrøm-Lang symposium today

Excellent speakers this year, as in previous years

[Olive Laprévote 🌻 @PestoFasta]

Let’s gooooooooo!!!! I have been waiting for the RC to test this baby, I’m so hyped!😍

[GIMP @GIMP_Official]

We are very happy to present GIMP 3.0.0 RC1! 🥳
Now is the time for everyone to test our first release candidate for what will be GIMP 3.0.0.

Result of years of work, we expect bugs (you should report!) but we hope you will still appreciate. 🤗

https://t.co/ces0cJulIm

[Olive Laprévote 🌻 @PestoFasta]

@DdelAlamo While impainting a short linker between two proteins with RFDiffusion, I noticed that if I allowed too few residues then it made crazy ω angles and neighboring Cα distances.
I used this to find what’s the minimal reslen for the linker, but long linkers could also get bananas.

[SBGrid: Structural Biology Software @SBGrid]

New Title Alert: Protkit- a Python library for structural bioinformatics, protein engineering, & machine learning.

Learn more here: https://t.co/BSGb2X5QUB

[Inkscape @inkscape]

Introducing Inkscape version 1.4!
New & updated features include Filter Gallery Dialog, Modular Grids, Swatches Dialog & more file import/export options. Power Users, this one's for you! Read all about 1.4: https://t.co/GeK1wZ98vZ #ArtWithOpenSource #Inkscape

[The Nobel Prize @NobelPrize]

BREAKING NEWS
The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”

[Martin Pacesa @MartinPacesa]

Have you ever wanted to design protein binders with ease? Today we present 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕, a user-friendly and open-source pipeline that allows to anyone to create protein binders de novo with high experimental success rates. @befcorreia @sokrypton

https://t.co/IPhMFpRgHh