An interaction-motif-based scoring function for protein-ligand docking

Background: A good scoring function is essential for molecular docking computations. In conventional scoring functions, energy terms modeling pairwise interactions are cumulatively summed, and the best docking solution is selected. Here, we propose to transform protein-ligand interactions into three-dimensional geometric networks, from which recurring network substructures, or network motifs, are selected and used to provide probability-ranked interaction templates with which to score docking solutions. Results: A novel scoring function for protein-ligand docking, MotifScore, was developed. It is non-energy-based, and docking is, instead, scored by counting the occurrences of motifs of protein-ligand interaction networks constructed using structures of protein-ligand complexes. MotifScore has been tested on a benchmark set established by others to assess its ability to identify near-native complex conformations among a set of decoys. In this benchmark test, 84% of the highest-scored d...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Zhong-Ru Xie, Ming-Jing Hwang
• Keywords: BMCBI 2010, Molecular Docking, Protein-ligand Interaction, Scoring Functions