Hugging Face's logo
Amelie Schreiber's picture
18 1 13

Amelie Schreiber

AmelieSchreiber
Sanyam52's profile picture Bayoubass's profile picture luckymanokc's profile picture
·
https://mastodon.social/@OctoNoodle

AI & ML interests

Diffusion and flow matching models for proteins, small molecules, DNA, and RNA, protein language models, machine translation, equivariant attention mechanisms, LoRA, and QLoRA.

Recent Activity

liked a model about 1 month ago
tattabio/gLM2_650M
liked a model about 1 month ago
tattabio/gLM2_150M
View all activity

Articles

Organizations

Blog-explorers's profile picture Social Post Explorers's profile picture

Posts 2

view post
Post
3942
A list of my favorite articles I've written on Hugging Face (the others are kind of mid imo):
https://huggingface.co./blog/AmelieSchreiber/a-new-era-of-enzyme-engineering

https://huggingface.co./blog/AmelieSchreiber/protein-optimization-and-design

https://huggingface.co./blog/AmelieSchreiber/rfdiffusion-potentials

https://huggingface.co./blog/AmelieSchreiber/mutation-scoring

https://huggingface.co./blog/AmelieSchreiber/esmbind

https://huggingface.co./blog/AmelieSchreiber/esm2-ptm

https://huggingface.co./blog/AmelieSchreiber/directed-evolution-with-esm2

https://huggingface.co./blog/AmelieSchreiber/intrinsic-dimension-of-proteins

https://huggingface.co./blog/AmelieSchreiber/plm-persistent-homology-msa-replacement

https://huggingface.co./blog/AmelieSchreiber/faster-pha
view post
Post
Currently attempting to hack EvoDiff to generate binders for target proteins with some interesting results. The generated binders tend to change conformation, sometimes drastically, when bound to the target proteins compared to their unbound states. Below is the target protein with an IDR linker, the generated binder, and the binder bound to the target protein with the IDR linker structure as predicted by ESMFold. Notice how the binder goes from being a solid alpha-helix, to being beta-sheets (in orange). That's quite a change in tertiary structure!

Collections 6

ESMBind (ESMB) for Protein Binding Sites
ESMBind (or ESMB) are LoRA finetuned ESM-2 models for predicting general binding sites and active sites of proteins based on sequence alone.