| Accuracy assessment of protein-based docking programs against RNA targets. | |
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MedLine Citation:
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PMID: 20481574 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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. |
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Authors:
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Yaozong Li; Jie Shen; Xianqiang Sun; Weihua Li; Guixia Liu; Yun Tang |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Journal of chemical information and modeling Volume: 50 ISSN: 1549-960X ISO Abbreviation: J Chem Inf Model Publication Date: 2010 Jun |
Date Detail:
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Created Date: 2010-06-28 Completed Date: 2010-09-24 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101230060 Medline TA: J Chem Inf Model Country: United States |
Other Details:
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Languages: eng Pagination: 1134-46 Citation Subset: IM |
Affiliation:
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Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Drug Discovery Ligands Molecular Dynamics Simulation* Nucleic Acid Conformation Protein Conformation Proteins / chemistry, metabolism* RNA / chemistry, metabolism* ROC Curve User-Computer Interface |
| Chemical | |
Reg. No./Substance:
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0/Ligands; 0/Proteins; 63231-63-0/RNA |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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