In apo-structure scenario, FMOPhore scans the 3D-structure of the protein binding site surface using a small library of different probes (fragments). The probes represent diverse set of pharmacophoric features. The rationale behind the small library of probes is to have a good coverage of all possible interaction bond types that are relevant to drug design pipeline; hydrogen bond acceptor, hydrogen bond donor, hydrophobic, pi-pi-stacking, pication stacking, salt-bridges, halogen bond, and water-bridges, (Supplementary files 1.). In both scenarios, the binding site scanning (Apo) or analysis of bound ligands (Holo), can be done in a static or dynamic mode to include protein flexibility.