PKAD-R: curated, redesigned and expanded database of experimental pKa values in proteins

Understanding pKa values in ionizable protein residues is critical for understanding fundamental protein properties, such as structure, function and interactions. We present a new version of PKAD, named PKAD-R, which is a curated database of experimentally determined protein pKa values. The database builds upon its predecessors, PKAD and PKAD-2, with significant updates and improvements through: (1) careful data curation to remove incorrect entries and consolidate redundant entries by offering alternative structures and pKa values for each unique residue (2) database redesign, to enhance its usability by adding additional information such as protein and species names, detailed notes, as well as sequence identity (3) database expansion through identification of 214 new (128 non-redundant) pKa entries from the literature. The database currently contains 877 unique pKa entries for wild type structures and 147 for mutant structures, however, we aim to keep updating the database with new entries. The PKAD-R database is available as a stand-alone downloadable file as well as web servers. The database is designed to provide both a set of pKa entries for unique residues suitable for machine learning applications, as well as modularity by providing alternative pKa values and structures, allowing the user to decide which entries to include.