---
license: cc-by-nc-4.0
---

# Protein2PAM models and training data

## Overview
This repo contains Protein2PAM models and training data.

For Python API, see:  

- GitHub repo: https://github.com/Profluent-AI/protein2pam
- Zenodo archive: https://zenodo.org/records/17843038

## Model Summary
PAM prediction models for CRISPR-Cas nucleases.

### Main Models

| Model Name       | Input Protein/Domain | CRISPR Type     | Samples  | 
|-------------------|---------------------|-----------------|----------|
| `cas8`            | Cas8 or Cas10d      | Type I          | 28,410   |
| `cas9`            | Cas9 PI-domain      | Type II         | 15,843   |
| `cas12`           | Cas12 protein       | Type V          | 1,720    |

### Additional Models

| Model Name       | Input Protein/Domain | CRISPR Type | Samples |
|------------------|----------------------|-------------|---------|
| `cas9_full`       | Cas9 protein        | Type II     | 15,843  |
| `cas9_full_nolit` | Cas9 protein        | Type II     | 15,731  |
| `cas9_pid_nolit`  | Cas9 PI-domain      | Type II     | 15,731  |
| `cas9_pid_nme`    | Cas9 PI-domain      | Type II     | 15,843  |
| `cas12_no_lit`    | Cas12 protein       | Type V      | 1,675   |


## Dataset Summary

Training data is stored in: `Profluent-Bio/protein2pam-training-data`

### Data Fields

| Field name        | Description                                            | Data type                 | Example |
|-------------------|--------------------------------------------------------|---------------------------|---------|
| cas_family        | CRISPR-Cas family classification                       | string                    | Cas8 |
| source            | Data source ('CRISPR-Cas Atlas' or Literature')        | string                    | CRISPR-Cas Atlas |
| protein_id        | Identifier for literature sequences                    | string or null            | null |
| citation          | Literature citation(s)                                 | string or null            | null |
| doi               | DOI for the associated publication                     | string or null            | null |
| protein_sequence  | Full amino acid sequence                               | string                    | MTFMILQALYRY...NQN |
| pid_sequence      | PAM-interacting domain sequence (Cas9 only)            | string or null            | null |
| pam_consensus     | Consensus PAM sequence                                 | string                    | TTC |
| pam_logo_acgt     | ACGT-ordered numerical matrix for PAM logo             | array of float arrays     | [[0.005, 0.008, 0.007, 0.01], ...] |
| type              | CRISPR-Cas type classification                         | string                    | Type I |
| subtype           | CRISPR-Cas subtype or effector family                  | string                    | Cas8 |


## Licensing

Models and data are licensed under the [Creative Commons Attribution–NonCommercial 4.0 International (CC BY-NC 4.0)](https://creativecommons.org/licenses/by-nc/4.0/). You may share and adapt the models for non-commercial use with appropriate attribution.


## Citation 
If you use Protein2PAM in your research, please cite the following preprint:   
[Nayfach, S., Bhatnagar, A., Novichkov, A., et al. (2025). Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data. bioRxiv.](https://www.biorxiv.org/content/10.1101/2025.01.06.631536v1)