Model Card for ProstT5 ProstT5 is a protein language model (pLM) which can translate between protein sequence and structure. Model Details Model Description ProstT5 (Protein structure sequence T5) is based on ProtT5 XL U50, a T5 model trained on encoding protein sequences using span corruption applied on billions of protein sequences. ProstT5 finetunes ProtT5 XL U50 on translating between protein sequence and structure using 17M proteins with high quality 3D structure predictions from the AlphaFoldDB. Protein structure is converted from 3D to 1D using the 3Di tokens introduced by Foldseek. In a first step, ProstT5 learnt to represent the newly introduced 3Di tokens by continuing the original span denoising objective applied on 3Di and amino acid (AA) sequences. Only in a second step, ProstT5 was trained on translating between the two modalities. The direction of the translation is indicated by two special tokens ("\ " for translating from 3Di to AAs, “\ ” for translating from AAs to 3Di). To avoid clashes with AA tokens, 3Di tokens were cast to lower case (alphabets are identical otherwise). Developed by: Michael Heinzinger (GitHub @mheinzinger; Twitter @HeinzingerM) Model type: En…
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