AlphaFastPPi: a fast AlphaFold-Multimer-based pipeline for high-throughput screening

Abstract

Motivation Discovering new protein-protein interactions (PPIs) across entire proteomes offers vast potential for understanding novel protein functions and elucidate system properties within or between an organism. While recent advances in computational structural biology, particularly AlphaFold-Multimer, have facilitated this task, scaling for large-scale screenings remains a challenge, requiring significant computational resources. Results Here we introduce AlphaFastPPi, a pipeline built upon AlphaFold-Multimer and AlphaPulldown. AlphaFastPPi is a streamlined pipeline which reduces resource consumption compared to other methods resulting in enhanced efficiency. This is achieved by lowering the minimum number of models required from five to one, while maintaining a good accuracy. This provides a more sustainable approach to PPI prediction. We demonstrate that this optimization does not compromise the accuracy of the method, offering a fast, efficient, and environmentally friendly solution for PPI predictions.