RP3Net: a deep learning model for predicting recombinant protein production in Escherichia coli

<h4>Motivation</h4>Recombinant protein expression can be a limiting step in the production of protein reagents for drug discovery and other biotechnology applications. We introduce RP3Net (Recombinant Protein Production Prediction Network), an AI model of small-scale heterologous soluble protein expression in Escherichia coli. RP3Net utilizes the most recent protein and genomic foundational models. A curated dataset of internal experimental results from AstraZeneca and publicly available data from the Structural Genomics Consortium was used for training, validation and testing of RP3Net.<h4>Results</h4>RP3Net achieves an increase in area under the receiver operator curve (AUROC) of 0.15, compared to a baseline model. When experimentally validated on an independent, prospective, manually selected set of 97 constructs, RP3Net outperformed currently available models, with an AUROC of 0.83, delivering accurate predictions in 77% of the cases, and correctly identifying successfully expressing constructs in 92% of cases.<h4>Availability and implementation</h4>The model, along with installation and running instructions, is available under an MIT licence at https://github.com/RP3Net/RP3Net, DOI 10.5281/zenodo.17243498.