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To eventually become an unofficial working Pytorch implementation of Alphafold2, the breathtaking attention network that solved CASP14. Will be gradually implemented as more details of the architecture is released. Once this is replicated, I intend to fold all available amino acid sequences out there in-silico and release it as an academic torrent, to further science. Deepmind has open sourced the official code in Jax, along with the weights! This repository will now be geared towards a straight pytorch translation with some improvements on positional encoding. lhatsk has reported training a modified trunk of this repository, using the same setup as trRosetta, with competitive results. The underlying assumption is that the trunk works on the residue level, and then constitutes to atomic level for the structure module, whether it be SE3 Transformers, E(n)-Transformer, or EGNN doing the refinement.
Features
- Predicting distogram, like Alphafold-1, but with attention
- You can also turn on prediction for the angles
- Predict coordinates
- MSA, ESM, or ProtTrans Embeddings
- Real-Value Distance Prediction
- Convolutions
Project Samples
