Acceptable antibody-antigen docking poses and trajectories and Boltz-2-derived models for AutoHMD benchmark

AutoHMD Supporting Dataset II This dataset accompanies the manuscript "AutoHMD: Scalable and Accurate Validation of Antibody–Antigen Complexes by Heated Molecular Dynamics" and serves as a companion record to AutoHMD Supporting Dataset I. The dataset contains additional Heated Molecular Dynamics (HMD) trajectories and structural models used to evaluate pose discrimination performance across experimentally derived and AI-generated antibody–antigen complexes. The deposited files include: acceptable_poses_pdbs.tar.xz: antibody–antigen complexes classified as acceptable-quality poses according to CAPRI criteria, curated from the docking set from AbSet. acceptable_packed_traj.tar.xz: HMD replicate trajectories corresponding to the acceptable-quality benchmark set. boltz_poses.tar.xz: structural models generated using Boltz-2 for independent validation of the AutoHMD workflow. boltz_high-quality_trajs.tar.xz: HMD trajectories of high-quality Boltz-generated complexes. boltz_acceptable_trajs.tar.xz: HMD trajectories of acceptable-quality Boltz-generated complexes. boltz_incorrect_trajs.tar.xz: HMD trajectories of incorrect Boltz-generated complexes. The acceptable-pose benchmark extends the evaluation beyond the binary distinction between high-quality and incorrect complexes, allowing assessment of intermediate-quality binding modes. The Boltz-generated antibody-antigen structures provide an independent validation set representative of AI-based structure prediction workflows. For the docking set, three independent HMD simulation replicates were performed, while for Boltz-generated poses five replicates were ran. Each replicate consists of 5,600 trajectory frames generated under progressive thermal perturbation. These simulations were used to investigate interface stability, monitor iRMSD evolution, characterize interaction persistence, and evaluate the robustness of AutoHMD across different pose-quality categories. Together with AutoHMD Supporting Dataset I, this record provides the complete benchmark dataset used in the development and validation of the AutoHMD framework. Associated manuscript: "AutoHMD: Scalable and Accurate Validation of Antibody–Antigen Complexes by Heated Molecular Dynamics". Associated GitHub: https://github.com/SFBBGroup/AutoHMD Associated repository: 10.5281/zenodo.22757671