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Amelie Schreiber

AmelieSchreiber

https://mastodon.social/@OctoNoodle

amelie_iska

Amelie-Schreiber

AI & ML interests

Protein language models, machine translation, equivariant attention mechanisms, LoRA, and QLoRA.

Articles

A Guide to Designing New Functional Proteins and Improving Protein Function, Stability, and Diversity with Generative AI

30 minutes ago

• 2

RFDiffusion Potentials

15 days ago

• 7

Predicting the Effects of Mutations on Protein Function with ESM-2

Dec 13, 2023

• 1

Faster Persistent Homology Alignment and Protein Complex Clustering with ESM-2 and Persistence Landscapes

Nov 30, 2023

Clustering Protein Complexes using Persistent Homology and Finetuning ESM-2 for PPI Network Prediction

Nov 29, 2023

ESM-2 for Generating and Optimizing Peptide Binders for Target Proteins

Nov 23, 2023

Persistent Homology Alignment (PHA): Replacing Multiple Sequence Alignments using ESM-2 and Persistent Homology

Nov 15, 2023

Predicting Protein-Protein Interactions Using a Protein Language Model and Linear Sum Assignment

Oct 15, 2023

• 3

ESMBind (ESMB) Ensemble Models

Sep 22, 2023

• 3

ESMBind (ESMB): Low Rank Adaptation of ESM-2 for Protein Binding Site Prediction

Sep 15, 2023

• 4

Organizations

Posts 1

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!