We provide two ways to use SaProt, including through huggingface class and through the same way as in esm github. Users can choose either one to use. The following code shows how to load the model. The esm version is also stored in the same folder, named SaProt650MAF2.pt. We provide a function to load the model. We provide a function to predict the mutational effect of a protein sequence. The example below shows how to predict the mutational effect at a specific position. If using the AF2 structure, we strongly recommend that you add pLDDT mask (see below). If you want to generate protein embeddings, you could refer to the following code. The embeddings are the average of the hidden states…