Fig. 4

Performance evaluation of the benchmarking methods for detecting the ADRP substrate-binding site. a The structures of the protein (green cartoon) at frame 30 (smallest RMSD compared to the crystallographic structure) of the ADRP domain trajectory with the corresponding cavities detected (gray surfaces) by each benchmarking method. b The total volume of the cavities detected in the ADRP substrate-binding site along the 600 ns simulation. The total volume is averaged in a window of 20 frames. The red dashed line indicates the molecular surface volume of the ADP-ribose molecule that originally occupied the ADRP substrate-binding site in the crystallographic structure (PDB ID: 6W02, chain B). c Elapsed time to detect and characterize ADRP substrate-binding site. The standard workflow of pyKVFinder, as in parKVFinder, detects cavities and applies spatial and constitutional characterizations. The full workflow of pyKVFinder comprises standard workflow with depth and hydropathy characterizations