AlignDockBenchmarck

AlignDockBench is a curated benchmark designed to evaluate template-
based molecular docking and 3D molecular alignment methods. It comprises 61 diverse
PL complex templates, each associated with a set of query complexes, totaling 369 PL
structures. Unlike widely used docking benchmarks which do
not include reference ligands, AlignDockBench provides co-crystallized template ligands
for each query, enabling the evaluation of methods that leverage a known reference to
guide 3D conformation prediction. To ensure target diversity, the 61 templates were se-
lected from the DUD-E and DEKOIS benchmarks, spanning major target classes
including kinases, proteases, nuclear receptors and GPCRs. For each template, query
PL complexes were mined from the Protein Data Bank (PDB) by identifying binding
pockets—defined as all residues within 12˚A of the ligand—that could be rigidly aligned
(translation + rotation) to the template pocket with a backbone Root Mean Square Devi-
ation (RMSD) below 1.2 Å, using TM-align. Query-template pairs were retained only
if the shape Tanimoto similarity exceeded 0.5 between the template and query ligands,
ensuring a minimum level of 3D structural superposition.