FlashPPI: Linear time prediction of proteome scale microbial protein interactions FlashPPI is a contrastively trained model for protein protein interaction (PPI) prediction, grounded in residue level interactions, that enables full proteome interaction prediction in minutes. By reframing PPI prediction as a dense retrieval task, FlashPPI circumvents the quadratic computational bottleneck of traditional all vs all structural screening. Scalable: Reduces proteome wide screening from days/months to minutes. Interpretable: Predicts fine grained, residue level 2D contact maps for retrieved interaction candidates. Genomic Priors: Leverages gLM2 to capture cross protein, multi gene co evolutionary signals. Web Server FlashPPI is integrated into seqhub.org. You can upload a FASTA and interactively explore whole proteome networks and contact maps. Explore an example network here. Usage See the github repo https://github.com/TattaBio/flashppi for usage and inference scripts. License The model code and inference scripts in the GitHub repo are licensed under the Apache License 2.0. The FlashPPI model weights are hosted on Hugging Face and released under the Creative Commons Attribution NonComm…
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