Reproducibility-Aware Evaluation of Web-Based Docking Servers with Decoupled Localization and Pose Fidelity Metrics

This dataset contains all input structures, docked pose files, per-run RMSD tables, and analysis scripts used in the study “Beyond Pose Accuracy: Reproducibility-Aware Evaluation of Web-Based Docking Servers.” Data are organized by docking server and protein class, with individual folders for each protein–ligand complex containing prepared receptor structures, reference ligands, docked poses from three independent runs, and corresponding RMSD outputs. Custom Python scripts used to calculate centroid distance, in-place RMSD, and aligned RMSD are included together with usage instructions. These files enable full reproduction of the reported analyses.