Virtual screening (VS) is a computationally intensive process crucial for drug discovery, often requiring significant resources to analyze large chemical libraries and predict ligand-protein interactions. This study evaluates the performance impact of containerization on METADOCK 2, a high-throughput docking software when deployed on heterogeneous high-performance computing (HPC) platforms. By testing three containerization technologies - Docker, Singularity, and Apptainer - across varying CPU and GPU configurations, the experiments reveal that containerization introduces negligible performance overhead, with deviations below 1%. Moreover, METADOCK 2 demonstrated the capability to efficiently process large molecular complexes, surpassing the limitations of commercial tools such as AutoDock Vina. The results underscore the advantages of container-based deployment for ensuring portability, reproducibility, and scalability in scientific computing. This study concludes that containerized METADOCK 2 is a robust and efficient solution for VS tasks on heterogeneous HPC platforms.