Evaluation of scoring function performance on DNA-ligand complexes

Pedro Fong, Hong Kong Wong

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


Background: 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. Objective: 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. Results: 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. Conclusion: 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.

Original languageEnglish
Pages (from-to)40-49
Number of pages10
JournalOpen Medicinal Chemistry Journal
Issue number1
Publication statusPublished - 2019


  • ASP
  • AutoDock
  • ChemScore
  • DNA-ligand complex
  • Docking
  • GoldScore


Dive into the research topics of 'Evaluation of scoring function performance on DNA-ligand complexes'. Together they form a unique fingerprint.

Cite this