{"title":"3dDNAscoreA: A scoring function for evaluation of DNA 3D structures.","authors":"Yi Zhang, Chenxi Yang, Yiduo Xiong, Yi Xiao","doi":"10.1016/j.bpj.2024.02.018","DOIUrl":null,"url":null,"abstract":"<p><p>DNA molecules are vital macromolecules that play a fundamental role in many cellular processes and have broad applications in medicine. For example, DNA aptamers have been rapidly developed for diagnosis, biosensors, and clinical therapy. Recently, we proposed a computational method of predicting DNA 3D structures, called 3dDNA. However, it lacks a scoring function to evaluate the predicted DNA 3D structures, and so they are not ranked for users. Here, we report a scoring function, 3dDNAscoreA, for evaluation of DNA 3D structures based on a deep learning model ARES for RNA 3D structure evaluation but using a new strategy for training. 3dDNAscoreA is benchmarked on two test sets to show its ability to rank DNA 3D structures and select the native and near-native structures.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.2000,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11393702/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biophysical journal","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1016/j.bpj.2024.02.018","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/2/26 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"BIOPHYSICS","Score":null,"Total":0}
引用次数: 0
Abstract
DNA molecules are vital macromolecules that play a fundamental role in many cellular processes and have broad applications in medicine. For example, DNA aptamers have been rapidly developed for diagnosis, biosensors, and clinical therapy. Recently, we proposed a computational method of predicting DNA 3D structures, called 3dDNA. However, it lacks a scoring function to evaluate the predicted DNA 3D structures, and so they are not ranked for users. Here, we report a scoring function, 3dDNAscoreA, for evaluation of DNA 3D structures based on a deep learning model ARES for RNA 3D structure evaluation but using a new strategy for training. 3dDNAscoreA is benchmarked on two test sets to show its ability to rank DNA 3D structures and select the native and near-native structures.
DNA 分子是重要的大分子，在许多细胞过程中发挥着基础性作用，在医学领域也有广泛的应用。例如，用于诊断、生物传感器和临床治疗的DNA适配体已被迅速开发出来。最近，我们提出了一种预测 DNA 三维结构的计算方法，称为 3dDNA。然而，该方法缺乏评估预测 DNA 3D 结构的评分函数，因此无法对用户进行排序。在此，我们报告了一种用于评估 DNA 3D 结构的评分函数 3dDNAscoreA，它基于用于 RNA 3D 结构评估的深度学习模型 ARES，但使用了一种新的训练策略。我们在两个测试集上对 3dDNAscoreA 进行了基准测试，以显示其对 DNA 3D 结构进行排序并选择原生和近似原生结构的能力。
期刊介绍：
BJ publishes original articles, letters, and perspectives on important problems in modern biophysics. The papers should be written so as to be of interest to a broad community of biophysicists. BJ welcomes experimental studies that employ quantitative physical approaches for the study of biological systems, including or spanning scales from molecule to whole organism. Experimental studies of a purely descriptive or phenomenological nature, with no theoretical or mechanistic underpinning, are not appropriate for publication in BJ. Theoretical studies should offer new insights into the understanding ofexperimental results or suggest new experimentally testable hypotheses. Articles reporting significant methodological or technological advances, which have potential to open new areas of biophysical investigation, are also suitable for publication in BJ. Papers describing improvements in accuracy or speed of existing methods or extra detail within methods described previously are not suitable for BJ.
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