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Amelie Schreiber

AmelieSchreiber
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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.

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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!

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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.