Datasets for "Unified Biomolecular Trajectory Generation via Pretrained Variational Bridge"

Yu Ziyang, Huang Wenbing and Liu Yang. (2026). Part of the datasets for "Unified Biomolecular Trajectory Generation via Pretrained Variational Bridge" published in ICLR 2026, including custom data splits for fine-tuning, as well as all raw data used for evaluation 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: 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. mdCATH Mirarchi, A., Giorgino, T., & De Fabritiis, G. (2024). mdCATH: A large-scale MD dataset for data-driven computational biophysics. Scientific Data, 11(1), 1299. MISATO Siebenmorgen, T., Menezes, F., Benassou, S., Merdivan, E., Didi, K., Mourão, A. S. D., ... & Popowicz, G. M. (2024). MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery. Nature computational science, 4(5), 367-378. PDBBind Wang, R., Fang, X., Lu, Y., & Wang, S. (2004). The PDBbind database: Collection of binding affinities for protein− ligand complexes with known three-dimensional structures. Journal of medicinal chemistry, 47(12), 2977-2980. Wang, R., Fang, X., Lu, Y., Yang, C. Y., & Wang, S. (2005). The PDBbind database: methodologies and updates. Journal of medicinal chemistry, 48(12), 4111-4119. Liu, Z., Li, Y., Han, L., Li, J., Liu, J., Zhao, Z., ... & Wang, R. (2015). PDB-wide collection of binding data: current status of the PDBbind database. Bioinformatics, 31(3), 405-412.