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Docking and scoring for nucleic acid-ligand interactions: Principles and current status
Yuyu Feng1, Yumeng Yan1, Jiahua He1
1School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.
Abstract:
Nucleic acid (NA)-ligand interactions have crucial roles in many cellular processes and, thus, are increasingly attracting therapeutic interest in drug discovery. Molecular docking is a valuable tool for studying molecular interactions. However, because NAs differ significantly from proteins in both their physical and chemical properties, traditional docking algorithms and scoring functions for protein-ligand interactions might not be applicable to NA-ligand docking. Therefore, various sampling strategies and scoring functions for NA-ligand interactions have been developed. Here, we review the basic principles and current status of docking algorithms and scoring functions for DNA/RNA-ligand interactions. We also discuss challenges and limitations of current docking and scoring approaches.
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