Vina-FPGA2: a high-level parallelized hardware-accelerated molecular docking tool based on the inter-module pipeline

• Vina-FPGA2 introduces an inter-module pipeline design that overcomes the irregular computation bottlenecks of AutoDock Vina, achieving significant performance gains. • It exploits task-level independence and a reinforcement learning-based resource allocation solver for efficient hardware implementation on FPGA. • On Xilinx UltraScale XCKU060, Vina-FPGA2-Enhanced achieves 12.6× speedup over CPU and 3.3× improvement over Vina-FPGA. • Compared to Vina-GPU, Vina-FPGA2 improves energy efficiency by 7.2×, making it a compelling low-power accelerator for molecular docking.