Fig. 4: Retrospective validation of protein residue mutation-free energy calculations (PRM-FEP+) for engineering kinome-wide selectivity.

a scanMAX plots for ligands in the retrospective analysis which includes representatives from our novel 5,6-cores (blue shaded) and 6,6-cores (purple shaded), as well as representatives from three known literature scaffolds (gray shaded) of Wee1 inhibitors (pyrazolopyrimidinone core, compound 6; pyrimidine-based tricyclic core^45,60, compound 7; and pyrimidopyrimidinone core²⁶, compound 8). For full-size scanMAX plots see Supplementary Information, Fig. SI-1. b Propensity of experimentally observed hits in the scanMAX panel according to gatekeeper (GK) family correlates to PRM-FEP+ pKi predictions for each of the seven ligands bound to mutant Wee1 binding pockets; i.e., each ligand modeled while perturbing from the WT Wee1 binding pocket to mutant binding pockets containing each of the five common gatekeeper mutations in turn (Asn376 → Thr, Phe, Met, Leu, and Val). scanMAX % kinases hit reflects the percentage of kinases with a given GK residue among the scanMAX kinases that have % Ctrl <10, with a minimum of 1% where \({{{\mathrm{\%}}}}{{{\mathrm{Ctrl}}}}{{=}}\frac{{{{\mathrm{test}}}}\; {{{\mathrm{compound}}}}\; {{{\mathrm{signal}}}}{{{\mathrm{-}}}}{{{\mathrm{positive}}}}\; {{{\mathrm{control}}}}\; {{{\mathrm{signal}}}}}{{{{\mathrm{negative}}}}\; {{{\mathrm{control}}}}\; {{{\mathrm{signal}}}}{{{\mathrm{-}}}}{{{\mathrm{positive}}}}\; {{{\mathrm{control}}}}\; {{{\mathrm{signal}}}}}\times 100\%\). Gatekeeper residue assignments across scanMAX kinases, raw scanMAX results and PRM-FEP+ predictions are provided as a Source Data Excel file.