Olive Laprévote 🌻

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!

TINY. SHOES. I repeat: TINY SHOES.

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 Throughout, the authors have balanced inclusivity (capturing a broad range of designs, including historic but unpublished examples) with rigorous hand-checking to maintain quality.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: nature.com/articles/s4158… Website: pragmaticproteindesign.bio.ed.ac.uk/pda/

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: su.varbi.com/en/what:job/jo…

🍂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

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 cdn.rcsb.org/rcsb-pdb/gener…

A picture speaks a thousand words. Air pollution is deadly. Displacing fossil fuels with nuclear energy saves lives.

@JeffreyRMillman Somewhat. Checking the PubPeer page (1) it appears the NSF tried it on freshly cut muscle tissues (2). 1: pubpeer.com/publications/8… 2: nsf-gov-resources.nsf.gov/files/USNSF-Ye…

Has anyone reproduced the 'transparent mouse' Science paper yet? I'm just curious (we haven't tried it yet) science.org/doi/10.1126/sc…

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

Our experience with #alphafold3 🤖 (code recently released) and some of our most recent #cryoEM 🔬 structures (thread below) nature.com/articles/s4158… nature.com/articles/s4146…

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

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: blender.org/download/relea… #b3d #DevFund

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: iopscience.iop.org/article/10.108…

Looking forward to see 260 participants at the 10th annual Linderstrøm-Lang symposium today Excellent speakers this year, as in previous years

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

@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.

A failure Ive noticed w RFdiffusion w big proteins is distorted backbone torsions outside normal Ramachandran space, which ProteinMPNN designs as polyglycines that arent accurately refolded. Curious if others have also seen this & if reducing Gly insertion improves designability

New Title Alert: Protkit- a Python library for structural bioinformatics, protein engineering, & machine learning. Learn more here: buff.ly/3zI2XQE

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: inkscape.org/news/2024/10/1… #ArtWithOpenSource #Inkscape

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.”

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 biorxiv.org/content/10.110…