Skip to main content
. Author manuscript; available in PMC: 2017 Jul 13.
Published in final edited form as: Annu Rev Biophys. 2017 Mar 15;46:227–246. doi: 10.1146/annurev-biophys-070816-033920

Table 2.

Summary of a selected set of ligand-RNA docking tools

Name/Reference Binding target(s) Descriptions
DrugScoreRNA (77, 113) RNA The knowledge-based scoring function contains a set of distance-dependent potentials between two atoms in ligand and flexible target, respectively.
MORDOR (61) RNA and Protein The CHARMM-27 and general AMBER force fields are applied to RNA and ligand, respectively. The model considers flexible conformations of the ligand and the RNA target.
DOCK6 (80) RNA and Protein An extended version is developed for targeting RNA. The physics-based scoring function contains the effects of solvation and sodium ion effects on docking.
ligandRNA (115) RNA The model scores and ranks ligand poses in ligand-RNA complexes. The knowledge-based function contains a set of distance- and angle-dependent statistical potentials for atom pairs between ligand and RNA.
rDOCK(104, 122) Nucleic acids and protein The package is open source. The scoring function is specifically developed for RNA-ligand docking by taking into account the stacking interactions and the charge-distributions in both RNA and ligand.