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| license: cc-by-nc-4.0 |
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| # FlashPPI: Linear-time prediction of proteome-scale microbial protein interactions |
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| **NEW: FlashPPI2 is the latest version of FlashPPI which includes training on high-confidence [**AFDB heterodimer complexes**](https://www.biorxiv.org/content/10.64898/2026.03.27.714458v1.full.pdf)**, improving AUPRC by 17% of the [tattabio/ecoli_pdb_benchmark](https://huggingface.co/datasets/tattabio/ecoli_pdb_benchmark) |
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| The original FlashPPI model is available at [tattabio/flashppi](https://huggingface.co/tattabio/flashppi). |
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| ## Web Server |
| FlashPPI is integrated into [seqhub.org](https://seqhub.org). You can upload a FASTA and interactively explore whole-proteome networks and contact maps. Explore an example network [here](https://seqhub.org/tattabio/mycobacterium_tb?ppi=true). |
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| ## Usage |
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| See the github repo https://github.com/TattaBio/flashppi for usage and inference scripts. |
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| ## License |
| The model code and inference scripts in the GitHub repo are licensed under the Apache License 2.0. |
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| The FlashPPI model weights are hosted on Hugging Face and released under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) license. The weights are freely available for academic and research purposes. |
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| ## Citing |
| If you use FlashPPI or our datasets in your research, please cite: |
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| ``` |
| @article{ |
| doi:10.1073/pnas.2610619123, |
| author = {Andre Cornman and Matt Tranzillo and Nicolo G. Zulaybar and Imane Bouzit and Yunha Hwang }, |
| title = {Linear-time prediction of proteome-scale microbial protein interactions}, |
| journal = {Proceedings of the National Academy of Sciences}, |
| volume = {123}, |
| number = {25}, |
| pages = {e2610619123}, |
| year = {2026}, |
| doi = {10.1073/pnas.2610619123}, |
| URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2610619123}, |
| eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2610619123}, |
| } |
| ``` |
