文献类型：期刊文献

英文题名：Accuracy Assessment of Protein-Based Docking Programs against RNA Targets

作者：Li, Yaozong[1];Shen, Jie[1];Sun, Xiangiang[1];Li, Weihua[1];Liu, Guixia[1];Tang, Yun[1]

机构：[1]E China Univ Sci & Technol, Dept Pharmaceut Sci, Sch Pharm, Shanghai 200237, Peoples R China

年份：2010

卷号：50

期号：6

起止页码：1134

外文期刊名：JOURNAL OF CHEMICAL INFORMATION AND MODELING

收录：;EI(收录号：20102613048374);WOS:【SCI-EXPANDED(收录号:WOS:000279069800016)】；

基金：The authors greatly appreciated Dr. Philip W. Lee for his kind help in improving the language of the manuscript. This work was supported by the Program for New Century Excellent Talents in University (grant no. NCET-08-0774), the 863 High-Tech Project (grant no. 2006AA020404), the 111 Project (grant no. B07023), and the National S&T Major Project of China (grant no. 2009ZX09501-001).

语种：英文

外文关键词：Gold - Binding energy - Proteins

摘要：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.