Paired residue prediction dependencies in ESM2

This code repository contains all materials required for creating and hosting the publication entitled, "Paired residue prediction dependencies in ESM2".

The publication is hosted at this URL.

Data Description

All input and output data are git-tracked in the repository.

Inputs:

• inputs/P00813.fasta: The amino acid sequence for human adenosine deaminase. Downloaded from the P00813 UniProt entry(https://www.uniprot.org/uniprotkb/P00813/entry).
• inputs/P00813.pdb: The AlphaFold-predicted structure for human adenosine deaminase. Downloaded from the P00813 UniProt entry(https://www.uniprot.org/uniprotkb/P00813/entry).

Outputs:

• logits_single.npz: Stores the raw logits of each ESM2 model for the single token mask library. NPZ is a Numpy file format for storing many arrays which can be accessed by key values. This file is calculated using Modal and is git-tracked to avoid expensive recomputation, and so the notebook can be run without needing to run anything using Modal. For details on usage, see how the publication uses it.
• logits_double.npz: Same as above, but for the double token mask library.

Reproduce

Please see SETUP.qmd.

Contribute

Please see CONTRIBUTING.qmd.