期刊
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
卷 105, 期 -, 页码 -出版社
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2021.107872
关键词
DNA aptamers; In silico; Structure prediction; Docking simulation; Modelling
类别
资金
- Ministry of Higher Education (MOE), Malaysia
- Innovation and Commercilization Centre (ICC), Universiti Teknologi Malaysia (UTM) [PRGS:ICC] [PY/2020/03762]
- Department of Bioscience, Faculty of Science, UTM
This study utilizes bioinformatics tools to analyze the structural parameters and ligand interaction of DNA aptamers, finding Mfold and RNA Composer to be commonly used tools for secondary and tertiary structure prediction, and ZDOCK and AutoDock as preferred docking simulation tools.
Aptamers are short oligonucleotides that possess high specificity and affinity against their target. Generated via Systematic Evolution of Ligands by Exponential Enrichment, (SELEX) in vitro, they were screened and enriched. This review covering the study utilizing bioinformatics tools to analyze primary sequence, secondary and tertiary structure prediction, as well as docking simulation for various aptamers and their ligand interaction. Literature was pooled from Web of Science (WoS) and Scopus databases until December 18, 2020 using specific search string related to DNA aptamers, in silico, structure prediction, and docking simulation. Out of 330 published articles, 38 articles were assessed in the analysis based on the predefined inclusion and exclusion criteria. It was found that Mfold and RNA Composer web server is the most popular tool in secondary and tertiary structure prediction of DNA aptamers, respectively. Meanwhile, in docking simulation, ZDOCK and AutoDock are preferred to analyze binding interaction in the aptamer-ligand complex. This review reports a brief framework of recent developments of in silico approaches that provide predictive structural information of ssDNA aptamer. (c) 2021 Elsevier Inc. All rights reserved.
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