XDock: A General Docking Method for Modeling Protein–Ligand and Nucleic Acid–Ligand Interactions

Molecular docking is an essential
computational tool in structure-based
drug discovery and the investigation of the molecular mechanisms underlying
biological processes. Despite the development of many molecular docking
programs for various systems, a universal tool that can accurately
dock ligands across multiple system types remains elusive. Meeting
the need, we developed XDock, a versatile docking framework built
for both protein–ligand and nucleic acid–ligand interactions.
XDock efficiently accounts for ligand flexibility by docking multiple
conformations of a ligand and flexibly refining the final binding
poses. It utilizes a distance geometric method for ligand sampling
and leverages our knowledge-based scoring functions for assessing
protein–ligand and nucleic acid–ligand interactions.
XDock has undergone extensive validations on diverse benchmarks of
protein–ligand and nucleic acid–ligand complexes and
was compared with six other docking methods, including DOCK 6, AutoDock
Vina, PLANTS, LeDock, rDock, and RLDock. In addition, XDock is also
computationally efficient and on average can dock a ligand within
1 min.