Unifying pKa and Protonation Prediction with Sequence-based Deep Learning

No longer available: look to https://zenodo.org/records/20089807 for dataset pKaCHU: A Curated Microscopic pKa Dataset pKaCHU (data that are Combined, Honed, and Updated) is a curated dataset of experimentally derived microscopic pKa values with ionization state annotations for small molecules. Dataset Overview 9,042 microscopic pKa entries Experimentally derived values Explicit protonated or deprotonated microstate pairs Canonicalized SMILES representations Purpose Experimental microscopic pKₐ data can be limited and inconsistently formatted across commonly used benchmarks. pKaCHU address these issues by: Removing “acidic/basic” terminology Standardizing protonation and deprotonation conventions Providing explicit microstate pair mappings Harmonizing formatting across literature sources File Contents This recode includes one dataset file (CSV format) with the following columns: “prefix” – indicates whether the entry is associated with protonation (“Prot”) or deprotonation (“Deprot”) “micropka input” – microstate pair in the format: protonated_SMILES>>deprotonated_SMILES “pKas” – list of the reported pKₐs; some have more than one pKa due to overlapping from different sources “average” – the average of the pKₐs if there is more than one pKₐ “citation” – the literature sources associated with the given molecule and pKₐ Citation If you use pKaCHU in your work, please cite: Infante, C.; et al. Unifying pKₐ and Protonation Prediction with Sequence-Based Deep Learning. Manuscript under preparation (2026). DOI: 10.5281/zenodo.18704856 License This dataset is released under the Creative Commons Attribution 4.0 International license