Finetune a codon-level language model with 30k tryptophan synthases, then generate diverse, functional, enzymes with broad substrate scopes. Théophile Lambert @jsunn-y.bsky.social @francesarnold.bsky.social www.biorxiv.org/content/10.1...

Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence–function relationships across protein engineering campaigns @francescazfl.bsky.social @jsunn-y.bsky.social @francesarnold.bsky.social @arianemora.bsky.social Paper: doi.org/10.1093/nar/... DB: enzengdb.org

An energy-based model of protein conformational space can be used to predict structure from sequence, sample from the conformational landscape, rank structures, and predict mutation effects. @sokrypton.org www.biorxiv.org/content/10.6...

Becoming a real Asian by making my kid practice Chinese characters and math while he waits for his Saturday cello class.

Train a model to identify circularly-permuted structural homologs, then use it to discover novel pairs of related proteins! @aidenosinetrip1 @abulnaga.bsky.social @sokrypton.org www.biorxiv.org/content/10.1...

A benchmark that measures whether protein language models can structural similarity even with low sequence similarity. A little shameless self-promotion: CARP does very well! @Zinnia__Ma www.biorxiv.org/content/10.1...

First Thanksgiving since 2021 that I haven't been sick!

Use quantitative in vitro mass spectrometry to measure temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains! Cydney Martell @savaslab.bsky.social @grocklin.bsky.social www.biorxiv.org/content/10.1...

You have until Dec 1 to apply to the bioml PhD research internship! This is where you apply to work with me, @alexijie.bsky.social @avapamini.bsky.social @lcrawford.bsky.social or Kristen Severson! (new) link and some instructions below apply.careers.microsoft.com/careers/job/...

You have until Dec 1 to apply to the bioml PhD research internship! This is where you apply to work with me, @alexijie.bsky.social @avapamini.bsky.social @lcrawford.bsky.social or Kristen Severson! (new) link and some instructions below apply.careers.microsoft.com/careers/job/...

How spicy is too spicy for a work potluck? Asking for a friend

Alternate between AlphaFold3 "hallucinations" and fixed-backbone sequence design to generate or optimize proteins. www.biorxiv.org/content/10.1...

Cambridge listservs are wild

Many sequence-fitness functions are factorizable in sequence space. Taking advantage of this enables more efficient optimization by shrinking the effective search space. James C Bowden, Sergey Levine @jlistgarten.bsky.social arxiv.org/abs/2511.03032

Design stable, folded proteins using only the 10 "ancient" amino acids. www.biorxiv.org/content/10.1...

Computrs usd a rstrictd alphabt to dsign protins that fold & “mak sns.”

Design stable, folded proteins using only the 10 "ancient" amino acids. www.biorxiv.org/content/10.1...

You should apply to do an internship with us! - Make sure you attach a research statement (we don't consider anybody with no statement for interviews) - The application site will probably go down for a day or two on Nov 17, and the link may change jobs.careers.microsoft.com/global/en/jo...

Structure - > sequence models have different phylogenetic (and biochemical) preferences than protein language models. www.biorxiv.org/content/10.1...

Are you a PhD student interested in ML and biology or health? Come do an internship with me, @avapamini.bsky.social, Alex Lu, @lcrawford.bsky.social, or Kristen Severson at MSRNE! Applications are due Dec 1: make sure you include a research statement! jobs.careers.microsoft.com/global/en/jo...

Come do an internship with us! Please apply

Are you a PhD student interested in ML and biology or health? Come do an internship with me, @avapamini.bsky.social, Alex Lu, @lcrawford.bsky.social, or Kristen Severson at MSRNE! Applications are due Dec 1: make sure you include a research statement! jobs.careers.microsoft.com/global/en/jo...

Alternate between predicting structure with AF3 and designing sequence with ProteinMPNN to generate proteins, including protein, small molecule and nucleic acid binders @yehlincho.bsky.social @sokrypton.org www.biorxiv.org/content/10.1...

Alternate between predicting structure with AF3 and designing sequence with ProteinMPNN to generate proteins, including protein, small molecule and nucleic acid binders @yehlincho.bsky.social @sokrypton.org www.biorxiv.org/content/10.1...

Protein language models can be finetuned to generate many novel structural folds Arjuna Subramanian, Matt Thomson www.biorxiv.org/content/10.1...

Test the activity of 300+ natural enzymes against 100+ substrates, discover 200+ new enzymatic reactions, and train machine learning models to predict which enzymes can do which reactions. @aepaton.bsky.social @gabegomes.bsky.social @alisonnarayan.bsky.social www.nature.com/articles/s41...

Test the activity of 300+ natural enzymes against 100+ substrates, discover 200+ new enzymatic reactions, and train machine learning models to predict which enzymes can do which reactions. @aepaton.bsky.social @gabegomes.bsky.social @alisonnarayan.bsky.social www.nature.com/articles/s41...

Combine multimer structure prediction and an antibody language model to design de novo antibodies with nanomolar binding affinity. @synbiogaolab.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.1...

Out of 7 papers in my NeurIPS Benchmarks and Datasets Track area, the PCs overruled my recommendation on 3?!

Genome language models can generate new, high-fitness bacteriophages! @samuelhking.bsky.social @claudiadriscoll.bsky.social @david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.1...

Out of 7 papers in my NeurIPS Benchmarks and Datasets Track area, the PCs overruled my recommendation on 3?!

Genome language models can generate new, high-fitness bacteriophages! @samuelhking.bsky.social @claudiadriscoll.bsky.social @david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.1...

The posting is unfortunately not super clear on this, but please apply if you want to do BioML research, especially around machine learning for molecular biology and bioengineering! I get sad if there are no applicants with this profile in the pool!

If you're an undergrad and want to intern with me, this is where you need to apply!

Train a protein structure predictor that can handle 29 non-canonical amino acids, then use it to design binders with non-canonical amino acids that reduce immunogenicity. @panhammarstrom.bsky.social @patrickbryant1.bsky.social www.biorxiv.org/content/10.1...

A joint sequence-structure diffusion model for transmembrane proteins! www.biorxiv.org/content/10.1...

A compelling review of how ML/AI could help in the quest to find an enzyme for every reaction. @jsunn-y.bsky.social @francescazfl.bsky.social Yueming Long @francesarnold.bsky.social www.cell.com/cell-systems...

Typical Ohio activity

Ramblings of a mad AC 1. If you're reviewing a benchmarks and dataset paper, you should look at the dataset and make sure it's not full of garbage. 2. Biological datasets are especially prone to subtle garbage.

The @uwproteindesign.bsky.social's experimental pipeline behind models like RFdiffusion and ProteinMPNN: - A rapid, scalable, pipeline for producing and characterizing proteins - A demultiplexing protocol for converting oligopools to clonal constructs Jason Qian @lfmilles.bsky.social Basile Wicky

Ramblings of a mad AC 1. If you're reviewing a benchmarks and dataset paper, you should look at the dataset and make sure it's not full of garbage. 2. Biological datasets are especially prone to subtle garbage.

A benchmark dataset of 614 experimentally characterized de novo designed monomers from 11 different design studies shows that: - deep learning structural metrics only weakly predict success - The score distribution is different for different types of structures @grocklin.bsky.social

MSA Pairformer efficiently extracts structure, protein-protein interactions, and mutation effects from MSAs by decomposing the effects of phylogeny and structural contacts. @yoakiyama.bsky.social Zhidian Zhang @milot.bsky.social @martinsteinegger.bsky.social @sokrypton.org

I just want to be a good area chair

My child's dinner - a scoop of peanut butter on a deli sandwich flavored potato chip - a scoop of peanut butter mixed into yogurt - a slice of ham - a tablespoon of melted mozzarella cheese - a round piece cut out of a slice of bread

- Model bacterial genomes as sequences of proteins - predict protein-protein interactions, operon structure, and protein function - infer phenotypic traits - design synthetic genomes with desired properties @macwiatrak.bsky.social @mariabrbic.bsky.social @andresfloto.bsky.social

Last year ESM-3 was the 1st PLM (if I recall correctly) to supplement naturally occurring seqs w/ synthetic inverse folding-derived seqs, but they failed to show any direct evidence of improvement. Its nice to finally see direct evidence of the benefit of including synthetic data during training

In 1965, Margaret Dayhoff published the Atlas of Protein Sequence and Structure, which collated the 65 proteins whose amino acid sequences were then known. Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.

Great idea for a dataset and task! Thanks for using and assessing out Prot-xLSTM

In 1965, Margaret Dayhoff published the Atlas of Protein Sequence and Structure, which collated the 65 proteins whose amino acid sequences were then known. Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.