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license: cc-by-nc-4.0 |
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# Protein2PAM models and training data |
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## Overview |
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This repo contains Protein2PAM models and training data. |
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For Python API, see: |
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- GitHub repo: https://github.com/Profluent-AI/protein2pam |
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- Zenodo archive: https://zenodo.org/records/17843038 |
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## Model Summary |
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PAM prediction models for CRISPR-Cas nucleases. |
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### Main Models |
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| Model Name | Input Protein/Domain | CRISPR Type | Samples | |
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|-------------------|---------------------|-----------------|----------| |
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| `cas8` | Cas8 or Cas10d | Type I | 28,410 | |
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| `cas9` | Cas9 PI-domain | Type II | 15,843 | |
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| `cas12` | Cas12 protein | Type V | 1,720 | |
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### Additional Models |
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| Model Name | Input Protein/Domain | CRISPR Type | Samples | |
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|------------------|----------------------|-------------|---------| |
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| `cas9_full` | Cas9 protein | Type II | 15,843 | |
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| `cas9_full_nolit` | Cas9 protein | Type II | 15,731 | |
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| `cas9_pid_nolit` | Cas9 PI-domain | Type II | 15,731 | |
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| `cas9_pid_nme` | Cas9 PI-domain | Type II | 15,843 | |
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| `cas12_no_lit` | Cas12 protein | Type V | 1,675 | |
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## Dataset Summary |
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Training data is stored in: `Profluent-Bio/protein2pam-training-data` |
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### Data Fields |
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| Field name | Description | Data type | Example | |
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|-------------------|--------------------------------------------------------|---------------------------|---------| |
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| cas_family | CRISPR-Cas family classification | string | Cas8 | |
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| source | Data source ('CRISPR-Cas Atlas' or Literature') | string | CRISPR-Cas Atlas | |
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| protein_id | Identifier for literature sequences | string or null | null | |
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| citation | Literature citation(s) | string or null | null | |
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| doi | DOI for the associated publication | string or null | null | |
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| protein_sequence | Full amino acid sequence | string | MTFMILQALYRY...NQN | |
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| pid_sequence | PAM-interacting domain sequence (Cas9 only) | string or null | null | |
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| pam_consensus | Consensus PAM sequence | string | TTC | |
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| pam_logo_acgt | ACGT-ordered numerical matrix for PAM logo | array of float arrays | [[0.005, 0.008, 0.007, 0.01], ...] | |
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| type | CRISPR-Cas type classification | string | Type I | |
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| subtype | CRISPR-Cas subtype or effector family | string | Cas8 | |
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## Licensing |
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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. |
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## Citation |
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If you use Protein2PAM in your research, please cite the following preprint: |
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[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) |
