RostLab

Predict protein structure and function using sequence, evolution & more! Operated by lab members.

[RostLab @rostlab]

Introducing ProtSpace: a tool for visualizing protein embeddings in 2D/3D! 🎨
https://t.co/Wh0tM5Uda8
Try it:
📦https://t.co/UvNd3BJayT
🌐https://t.co/s8AQ6zGYkZ
#Proteomics #DataViz

[Elodie Laine @LaineElodie]

Very happy to introduce VespaG, for ultra-fast and accurate prediction of protein mutational effects. https://t.co/nyVOyZKrjo. Big thanks to @LiniMuc, Julius Schlensok, and @MarinaAbakarova for the great work and effort. Exciting collab with @rostlab 1/5

[RostLab @rostlab]

@JamesPBLloyd @DdelAlamo @daniela_barilla So far, we support only single sequences, but thanks for the suggestion!

[RostLab @rostlab]

@JamesPBLloyd @DdelAlamo @daniela_barilla Yes, each frame is a structure prediction of a point mutation. We recommend using ESMFold instead of AF2, which we have shown in previous work to be more sensitive. It's a lot faster as well.
However, MutAmore can interface with any structure predictor that outputs PDB files.

[RostLab @rostlab]

@DdelAlamo Thanks for sharing, Diego!
Here is a playlist with a couple more example movies: https://t.co/9wKSs0cDtH

[Michael Heinzinger @HeinzingerM]

Our new bilingual protein language model (pLM), ProstT5, translates between protein sequence and structure. Besides producing more structure-aware embeddings that are better at remote homology detection than sequence-pLMs, its translation capability enables inverse folding.

[RostLab @rostlab]

3/3 This study showcases the combined power of cutting-edge AI, traditional phylogenetics and manual annotations to unravel complex biological phenomena, such as evolution of protein function. Stay tuned for more! 📚🌟 #ScienceTwitter #Toxinology

[RostLab @rostlab]

1/3 🐍🧬 Exciting breakthrough in #SnakeToxins research published in #NatureCommunications! An international team led by Rostlab members unlocked the mysteries of three-finger toxins (3FTxs), from the venom of caenophidian snakes. 🔬#VenomResearch https://t.co/P28ruLZkl9

[RostLab @rostlab]

2/3 🔍Immediate ancestor of these toxins? A non-secretory, non-toxic Ly6, unique to squamate reptiles. Mechanism? Exon duplication followed by mutation led to novel forms with a membrane anchoring domain lost. 🧩 #Evolution #ReptileScience

[Noelia Ferruz @ferruz_noelia]

We (@lindner_seb, @HeinzingerM) introduce REXzyme, a new model for the generation of enzymes that catalyze user-defined chemical reactions. We'd like that the community can benefit as soon as possible from it, so we made it available in HuggingFace: https://t.co/tm526yit5D.

[RostLab @rostlab]

Mar 03 - Oberseminar: This is only a test https://t.co/5zATuvtMgc

[RostLab @rostlab]

Synteny analyses, phylogenetics and pLMs reveal that 3-finger-toxins evolved from a transmembrane "pre-3FTx" ancestor that gained increased affinity for nAChRs and lost its transmembrane region. #snakevenom #geneevolution #machinelearning

[RostLab @rostlab]

Did you know that 3-finger toxins in snake venoms evolved from a non-secretory ancestor? Our new preprint explores this gene family's evolution. Check it out here: https://t.co/Sgz5Qj8UgG #geneevolution #proteinlanguagemodels #transmembranehelices

[RostLab @rostlab]

Contrary to previous hypotheses, our research suggests that 3-finger toxins in snake venoms evolved from a single-copy gene unique to Toxicofera reptiles, not monomeric neuromodulatory Ly6s like LYNXs or SLURPs. #snakevenom #geneevolution #proteinfamily

[Elodie Laine @LaineElodie]

Is ColabFold's MMseqs2-based MSA generation protocol suitable for mutational outcome prediction? Yes! Joint work by @MarinaAbakarova and Céline Marquet. 1/2

[RostLab @rostlab]

EMBER3D can predict mutated structures of all single amino-acid variants in an average length protein in a matter of minutes. When correlated with deep mutational scanning experiments, EMBER3D predictions are much more sensitive to small changes in sequence than other systems.

[RostLab @rostlab]

EMBER3D predicts protein structure in fractions of a second with high sensitivity to small changes in sequence.
Protein Mutation Movies (PMMs) visually capture the effects of amino-acid substitutions.
https://t.co/IhgXEMidFW via @YouTube

[RostLab @rostlab]

Trading accuracy for speed, EMBER3D runs orders of magnitude faster than competing models while maintaining reasonable performance (although nowhere close to Alphafold2).