Evaluation of Scoring Function Performance on DNA-ligand Complexes

Pedro Fong*, Hong-Kong Wong
School of Health Sciences, Macao Polytechnic Institute, Macao, China

© 2019 Fong and Wong.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: ( This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this authors at the School of Health Sciences, Macao Polytechnic Institute, Meng Tak Building, Room 705, Rua de Luís Gonzaga Gomes, Macao, China; Tel: +85385993427; Fax: +85328753159;



DNA has been a pharmacological target for different types of treatment, such as antibiotics and chemotherapy agents, and is still a potential target in many drug discovery processes. However, most docking and scoring approaches were parameterised for protein-ligand interactions; their suitability for modelling DNA-ligand interactions is uncertain.


This study investigated the performance of four scoring functions on DNA-ligand complexes.

Material & Methods:

Here, we explored the ability of four docking protocols and scoring functions to discriminate the native pose of 33 DNA-ligand complexes over a compiled set of 200 decoys for each DNA-ligand complexes. The four approaches were the AutoDock, ASP@GOLD, ChemScore@GOLD and GoldScore@GOLD.


Our results indicate that AutoDock performed the best when predicting binding mode and that ChemScore@GOLD achieved the best discriminative power. Rescoring of AutoDock-generated decoys with ChemScore@GOLD further enhanced their individual discriminative powers. All four approaches have no discriminative power in some DNA-ligand complexes, including both minor groove binders and intercalators.


This study suggests that the evaluation for each DNA-ligand complex should be performed in order to obtain meaningful results for any drug discovery processes. Rescoring with different scoring functions can improve discriminative power.

Keywords: ASP, AutoDock, ChemScore, Docking, GoldScore, DNA-ligand complex.