Boltzina: Efficient and Accurate Virtual Screening via Docking-Guided Binding Prediction with Boltz-2

Abstract

In structure-based drug discovery, virtual screening using conventional molecular docking methods can be performed rapidly but suffers from limitations in prediction accuracy. Recently, Boltz-2 was proposed, achieving extremely high accuracy in binding affinity prediction, but requiring approximately 20 seconds per compound per GPU, making it difficult to apply to large-scale screening of hundreds of thousands to millions of compounds. This study proposes Boltzina, a novel framework that leverages Boltz-2's high accuracy while significantly improving computational efficiency. Boltzina achieves both accuracy and speed by omitting the rate-limiting structure prediction from Boltz-2's architecture and directly predicting affinity from AutoDock Vina docking poses. We evaluate on eight assays from the MF-PCBA dataset and show that while Boltzina performs below Boltz-2, it provides significantly higher screening performance compared to AutoDock Vina and GNINA. Additionally, Boltzina achieved up to 11.8$\times$ faster through reduced recycling iterations and batch processing. Furthermore, we investigated multi-pose selection strategies and two-stage screening combining Boltzina and Boltz-2, presenting optimization methods for accuracy and efficiency according to application requirements. This study represents the first attempt to apply Boltz-2's high-accuracy predictions to practical-scale screening, offering a pipeline that combines both accuracy and efficiency in computational biology. The Boltzina is available on github; https://github.com/ohuelab/boltzina.