Shocked pikachu face

Complete computational design of high-efficiency Kemp elimination enzymes - Nature We present a computational approach to the design of high-efficiency enzymes with catalytic parameters comparable to natural enzymes, enabling programming of stable, high-efficiency, new-to-nature Kem...

De novo design of a theozyme with catalytic efficiencies similar to natural ones— another milestone in computational design!

www.nature.com/articles/s41...

I really like the idea that with respect to learning "effort is the algorithm". When doing math problems you knew not to check the back of the book!

Does negging work on VCs?!?

Then why the seeds so big 😭

Stabilized designs of the malaria adhesin protein PvRBP2b for use as a potential diagnostic for Plasmodium vivax Plasmodium vivax is emerging as the most prevalent species causing malaria outside Africa. Most P. vivax infections are relapses due to the reactivation of the dormant liver stage parasites (hypnozoit...

Stabilized PvRBP2b variants - wonderful collab with Sarel Fleishman

🔥Increased yields and thermal stability

✌️Maintains human mAb recognition

🩸Sensitivity as a sero-diagnostic for P. vivax

💕 Editors Pick

👨🏻‍🔬First paper for PhD student Jaison

Please read & repost!

www.jbc.org/article/S002...

Has got to be the #1 biological 🤯

Paratope, I should say.

Love the masked epitope approach– lots of room for expanding on the idea.

Computational and Experimental Exploration of Protein Fitness Landscapes: Navigating Smooth and Rugged Terrains Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly a...

dealing with the ruggedness of protein fitness landscapes is perhaps the most challenging aspect of protein design and engineering - here we have written a short perspective about it - it's complicated and not perfectly understood but very interesting!

arxiv.org/abs/2411.12957

Another very nice database, this time of ADCs searchable by antibody, payload, linker, sequence similarity and includes preclinical and clinical data!

Second most common antigen is DLL3!

adcdb.idrblab.net

AACDB: Antigen-Antibody Complex Database — a Comprehensive Database Unlocking Insights into Interaction Interface Antibodies play a crucial role in the vertebrate immune system and have diverse biomedical applications. Understanding the intricate interactions between antibodies and antigens is an important step i...

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

Nice database of curated antibody:antigen complex structures.

i.uestc.edu.cn/AACDB/

Me please : )

I think it's just the effect of low hanging fruit having been picked and people moving onto fresh pastures. Enzyme design has always been a kind of holy grail in protein design though.

Didn't even know this was a thing!

#GoodThingsComeToThoseWait Sorry it's taking us a while. Promise that the wait will be well worth it! #OpenFold3 Love all the great work that's already been done #HelixFold3 #Ligo #Chai1 #Protenix #Boltz1

Preschools
Previous point about testing training set Kcat notwithstanding, 5x doesn't sound like a particularly high bar? That's just one okay substitution. Or do you mean a "fully novel" sequence?

Would love to be added!

Would love to join : )

RFam design method

Activity characterization

Characterization of A1 activity.

The Baker lab seems serious about moving into enzyme design.

Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.

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

New GPU-based MMseqs2: 20x faster searches on a single L40S (approx. as fast as a RTX 4090) vs. a 128-core CPU. This work enables to set up a very cost-efficient ColabFold MSA GPU server. 🧵🧵
📄 www.biorxiv.org/content/10.1...
💾 mmseqs.com
🗞️ developer.nvidia.com/blog/boost-a...

A close-up view of freshly-cooked shell pasta (Annie's white mac & cheese) with green peas (previously frozen). There are a smaller number of peas than shells, but each is nestled snuggly in a shell as if purposely stuffed

Strong receptor-ligand binding affinity
#ChemistsWhoCook

This is the one I've been waiting for! Generation of small molecule binders is a major limitation to biosensor development. This will unlock many things from research tools to diagnostics and therapeutics.