between a protein and a ligand is essential for binding. Energetically preferred positions of ligand atom types can be captured using a discriminatory function (Figure ). Docking of seed fragments to the binding site grid is performed by moving seed's rotational grid over the binding site grid points. Docked fragment poses that are in a steric clash with the protein are rejected (Figure ). A steric clash is considered if any interatomic distance between the fragment and the protein falls within ninetenths of the atoms' respective van der Waals sum. Each fragment translation and rotation that passes this initial filter is then evaluated with the RMR6 discriminatory function . Finally, greedy clustering of docked and scored fragment poses in the Root Mean Square Deviation (RMSD) space computed based on their heavy atoms at 2 Å cluster cutoff is performed, resulting in a uniform distribution of locally best-scoring docked seed fragments covering the entire protein binding site (Figure ).