Six-target docking poses and MD-scores for runtime-steered ultrashort molecular dynamics

This dataset accompanies the manuscript “Runtime-steered ultrashort molecular dynamics enables million-pose protein–ligand screening.” The release contains docking-pose data and processed molecular-dynamics outputs for six protein targets: EGFR, PTPN1, ERK2, PPARG, BACE1, and p38. The released dataset comprises 10,096 unique docking poses. The release includes: AutoDock Vina docking-pose PDBQT files; pose-level AutoDock Vina docking scores; pose-level MD-scores calculated from 5-ns simulations with five independent initial velocities; RMSD time-series data from the corresponding MD simulations; project-specific identifiers linking docking poses, MD-score tables, and RMSD time-series files; file manifests, data dictionaries, and SHA-256 checksums. Each released pose is assigned a public_pose_index, and each docking PDBQT file is assigned a public_docking_file_index. Together with the MODEL number and relative PDBQT path provided in the metadata, these identifiers allow the corresponding PDBQT structure, docking score, MD-score, and RMSD time-series data to be linked across the released files. MD trajectory files (XTC/GRO) are not included because of their large total data size. They are retained by the authors and may be made available upon reasonable request, subject to the authors’ data-sharing policy. The generated EGFR-focused million-pose library, the prospective MARV NP screening dataset, and experimental compound-library structures are not included in this release. Version 2 removes third-party binding-activity values, activity-derived labels, and related external-database identifiers from the public files to comply with source-database redistribution terms. The released files are limited to project-generated docking and molecular-dynamics outputs, together with project-specific identifiers required to link the released data.