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Dataset of knotted and unknotted proteins created by diffusion models
This dataset supports Unveiling the Entangled Landscape of Artificial Knotted Proteins ICLR poster and related GitHub repo.
The dataset contains a mixture of proteins generated by RFdiffusion+pMPNN, EvoDiff and a fraction of real proteins. For each of the three, the dataset contains 1k of knotted proteins and 4k of unknotted proteins.
Each protein has:
- sequence
- label with either 0 (unknotted protein) or 1 (knotted one)
- tool meaning one of the three approaches of getting the protein (RFdiffusion+pMPNN / EvoDiff / real protein)
- 1024 numbers being ProtBERT-BFD (protein language model) embeddings, which were used further in our paper
Predicted structures of the artificially generated proteins can be found at https://drive.google.com/file/d/1lxB7vmXkCrgbE2DrVkCi0cdFOkaQNF79/view?usp=sharing
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