This data set includes the full, all-vs-all kinase-substrate assignments by the IV-KAPhE method for the entire human phosphoproteome (union of the PhosphoSitePlus human phosphosite database and the Ochoa et al. 2020 high-confidence human phosphoproteome). This is an unfiltered version of Supplemental Table S1 from Invergo BM (2022) "Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data". The data set also includes files to facilitate scoring new human phosphosites, particularly the in vitro half of the IV-KAPhE model. "naive-bayes-plus-model.tar.gz" is an archive of HDF5 files comprising the "Naive Bayes+" multi-label, in vitro kinase-substrate assignment model used in the IV-KAPhE model, as described in the manuscript. These files are to be used with the motif-kit software package and can be used to score new sites. "kinase-int-domains-sig.tsv" and "kinase-sub-domains-sig.tsv" contain Pfam domains enriched among each kinase's interacting partners or substrates, respectively. Finally, "human-kinase-interactions.tsv" and "human-kinase-2nd-interactions.tsv" contain physical interactions and indirect ("2 hop") interactions between human protein kinases and other proteins, as described in the manuscript.