The Molecular Dynamics Dataset (MDD) comprises 231 unique targets (Figure ) from 862 protein-ligand complexes, sourced from the PDBBind collection v2020 . Only complexes with well-defined active sites and ligands with unambiguous affinity values (-log Ki, Kd and IC50) were considered. More details on the filtering procedure, functional composition and similarity assessments of MDD targets and ligands are available in Supplementary materials. MD simulation procedure MD preparation protocol, identical for all MDD complexes, is detailed in the supplementary materials. Briefly, MD simulations were executed using the GROMACS , utilizing a cubic box with periodic boundary conditions and a TIP3P water model. An initial minimization cycle, followed by temperature equilibration in the NVT ensemble and pressure equilibration in the NPT ensemble was carried out. Production simulations were conducted over a 200 ns timeframe, with a timestep of 100 ps.