Extended Data Fig. 3: Detailed workflow of the CAGE-prox strategy.
From: Time-resolved protein activation by proximal decaging in living systems
To prepare the initial structure for CAGE-prox calculation, an optimized protein–ligand complex structure was obtained from the PDB, and comparative modelling and/or ligand-docking were used when necessary. Geometry and energy parameters (D, A, ∆Gf and ∆∆Gb) were calculated by Rosetta and used as filters to exclude undesired sites. The sites that successfully passed the filters are considered as the ‘recommended sites’. In the next experimental validation step, ONBY was incorporated into the recommended sites followed by protein activity characterization with and without photo-activation.
