title: Accuracy assessment of protein-based docking programs against RNA targets.
abstract: Ribonucleic acid (RNA) molecules play central roles in a variety of biological processes and, hence, are attractive targets for therapeutic intervention. In recent years, molecular docking techniques have become one of the most popular and successful approaches in drug discovery; however, almost all docking programs are protein based. The adaptability of popular docking programs in RNA world has not been systematically evaluated. This paper describes the comprehensive evaluation of two widely used protein-based docking programs--GOLD and Glide--for their docking and virtual screening accuracies against RNA targets. Using multiple docking strategies, both GOLD 4.0 and Glide 5.0 successfully reproduced most binding modes of the 60 tested RNA complexes. Applying different docking/scoring combinations, significant enrichments from the simulated virtual and fragment screening experiments were achieved against tRNA decoding A site of 16S rRNA (rRNA A-site). Our study demonstrated that current protein-based docking programs can fulfill general docking tasks against RNA, and these programs are very helpful in RNA-based drug discovery and design.
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
authors.forename: Yaozong
authors.initials: Y
authors.lastname: Li
authors.forename: Jie
authors.initials: J
authors.lastname: Shen
authors.forename: Xianqiang
authors.initials: X
authors.lastname: Sun
authors.forename: Weihua
authors.initials: W
authors.lastname: Li
authors.forename: Guixia
authors.initials: G
authors.lastname: Liu
authors.forename: Yun
authors.initials: Y
authors.lastname: Tang
mesh_terms: D055808:Drug Discovery; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012372:ROC Curve; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins; D012313:RNA