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How Good Are Current Docking Programs at Nucleic Acid–Ligand Docking? A Comprehensive Evaluation by Dejun Jiang; Huifeng Zhao; Hongyan Du; Yafeng Deng; Zhenxing Wu; Jike Wang; Yundian Zeng; Haotian Zhang; Xiaorui Wang; Jian Wu; Chang-Yu Hsieh; Tingjun Hou is a Physics and Astronomy article available to read on EtoBox.

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Nucleic acid (NA)-ligand interactions are of paramount importance in a variety of biological processes, including cellular reproduction and protein biosynthesis, and therefore, NAs have been broadly recognized as potential drug targets. Understanding NA-ligand interactions at the atomic scale is essential for investigating the molecular mechanism and further assisting in NA-targeted drug discovery. Molecular docking is one of the predominant computational approaches for predicting the interactions between NAs and small molecules. Despite the availability of versatile docking programs, their performance profiles for NA-ligand complexes have not been thoroughly characterized. In this study, we first compiled the largest structure-based NA-ligand binding data set to date, containing 800 noncovalent NA-ligand complexes with clearly identified ligands. Based on this extensive data set, eight frequently used docking programs, including six protein-ligand docking programs (LeDock, Surflex-Dock, UCSF Dock6, AutoDock, AutoDock Vina, and PLANTS) and two specific NA-ligand docking programs (rDock and RLDOCK), were systematically evaluated in terms of binding pose and binding affinity predicti

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Author

Dejun Jiang; Huifeng Zhao; Hongyan Du; Yafeng Deng; Zhenxing Wu; Jike Wang; Yundian Zeng; Haotian Zhang; Xiaorui Wang; Jian Wu; Chang-Yu Hsieh; Tingjun Hou

Publisher

American Chemical Society (ACS)

Published

2023

Language

EN

Field

Physics and Astronomy (Physical Sciences)