The crystal structure whose co-crystallized ligand defines the reference pose. Pose RMSD is measured in this receptor frame without re-fitting the ligand, and is corrected for symmetry-equivalent atoms. Leave the residue name empty to use the largest bound ligand (waters, ions, buffers, lipids and glycans are skipped).
Use when the ligand is not a HETATM residue of the complex. Coordinates must be in the complex frame.
Poses of the crystal ligand docked back into its own receptor (SDF, PDBQT or PDB; up to 50 files). The top-ranked pose must fall within the RMSD threshold for the protocol to pass. To prepare, box and redock the ligand automatically before screening a library, start from the validate-then-screen workflow.
2 Å is the conventional redocking pass threshold. Best-of-top-k reports whether a near-native pose was sampled even when the scoring function ranked it lower.
Binding-Site Detector boxes used for docking. The box nearest the crystal ligand is reported; without one, a box is drawn around the crystal ligand.
Analogs crystallized with the same target, docked into the reference receptor. Each analog's complex is superposed onto the reference by its Cα atoms, and its crystal ligand is compared with the docked poses in that frame. Up to 10 analogs, 20 pose files each.
Docked poses of known actives and decoys, one file per molecule (up to 100), plus a CSV with id,active columns matching the file names. Each molecule is ranked by its best pose score to give EF1%, EF5%, ROC-AUC and BEDROC (α = 80.5); tied scores share their rank.