Sampling antibody conformational ensembles with ABodyBuilder4-STEROIDS Dataset

This repository contains molecular dynamics simulation data associated with the publication "Sampling antibody conformational ensembles with ABodyBuilder4-STEROIDS" (Spoendlin et al. - 2026). The data provided include MD trajectories and topology files generated using all-atom explicit-solvent MD for 91 experimentally resolved antibody structures. Four replica were run for 300 ns for each of the systems. We include: production trajectory (.nc), solvated and equilibrated topology files (.pdb), energy data (.csv), and restart checkpoints. Please refer to the manuscript for additional methodological details. Simulations were performed using OpenMM with the Amber19SB force field and TIP3P-FB water model. Production runs were performed in the NPT ensemble at 298 K for 300 ns per replica and per system. Trajectories were post-processed using CPPTRAJ. Periodic boundary condition artefacts were corrected. Water molecules and ions were stripped from the trajectories prior to deposition, retaining only protein coordinates. RMS fitting to the first frame was applied before writing the final stripped trajectories.