Datasets for "UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules"

Yu Ziyang, Huang Wenbing and Liu Yang. (2025). Part of datasets for "UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules" published in ICML 2025, including train/valid sets of PepMD & PDB, as well as all test sets used in the paper. If you plan to use the datasets we have released for training or evaluation, please ensure to properly cite the original source of these datasets: PDB Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., ... & Bourne, P. E. (2000). The protein data bank. Nucleic acids research, 28(1), 235-242. ATLAS Vander Meersche, Y., Cretin, G., Gheeraert, A., Gelly, J. C., & Galochkina, T. (2024). ATLAS: protein flexibility description from atomistic molecular dynamics simulations. Nucleic acids research, 52(D1), D384-D392. PepMD Yu, Z., Huang, W., & Liu, Y. (2024). Force-guided bridge matching for full-atom time-coarsened dynamics of peptides. arXiv preprint arXiv:2408.15126. Yu, Z., Huang, W., & Liu, Y. (2025). UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules. In Forty-second International Conference on Machine Learning. MD22 Chmiela, S., Vassilev-Galindo, V., Unke, O. T., Kabylda, A., Sauceda, H. E., Tkatchenko, A., & Müller, K. R. (2023). Accurate global machine learning force fields for molecules with hundreds of atoms. Science Advances, 9(2), eadf0873.