Ensembits is the first tokenizer of protein conformational ensembles that outperforms static tokenizers on RMSF prediction and matches them on function and mutation tasks while using less pretraining data.
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PLASMA applies regularized optimal transport with Sinkhorn iterations to produce fast, interpretable residue-level alignments and similarity scores between protein structures.
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ENSEMBITS: an alphabet of protein conformational ensembles
Ensembits is the first tokenizer of protein conformational ensembles that outperforms static tokenizers on RMSF prediction and matches them on function and mutation tasks while using less pretraining data.
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Fast and Interpretable Protein Substructure Alignment via Optimal Transport
PLASMA applies regularized optimal transport with Sinkhorn iterations to produce fast, interpretable residue-level alignments and similarity scores between protein structures.