A tale of two states: AlphaFold binding pockets on the apo–holo continuum — data

Data behind the manuscript A tale of two states: AlphaFold binding pockets on the apo–holo continuum: the apo/holo classification of 464,869 AHoJ-DB v2c entries and the 237,922-pocket analysis set with released and size-balanced labels; the unified-binding-site tables at every clustering level; the binding-site detection (P2Rank, fpocket, IF-SitePred), docking (Uni-Dock) and AlphaFill transplant results on the AlphaFold DB version 4 models; the tables from which every figure is drawn and the outputs behind every supplementary table; the two single-atom ligand lists (Supplementary Data 1); and the exact AlphaFold DB version 4 model files used, with a checksum manifest. README.md in the record describes every file. Per-entry plots and classification JSON files are served by the AHoJ web resource (https://dev.apoholo.cz, moving to https://apoholo.cz). Code: https://github.com/ioChris/ahoj-alphafold. Funding: this work was supported by the ELIXIR CZ Research Infrastructure (ID LM2023055, MEYS CR). Computational resources were provided by the e-INFRA CZ project (ID:90254), supported by the Ministry of Education, Youth and Sports of the Czech Republic.