Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction
Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction
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DOI：
10.1093/bioinformatics/btl059
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发表时间：
2006-04-15
期刊：
影响因子：
5.8
通讯作者：
Beveridge, DL
中科院分区：
文献类型：
--
作者：
Dixit, SB;Beveridge, DL
我们报道了一个基于网络的工具(MDDNA)的发布，该工具基于从一组涉及所有独特的四核苷酸的DNA序列的分子动力学(MD)轨迹中提取的数据来研究和模拟DNA的精细结构细节。动态网络界面可用于分析第一邻近序列上下文对DNA的10个唯一二核苷酸步骤的影响。包括基于MD结果构建任何用户定义序列的所有原子模型的功能。这个界面的后端是一个关系数据库，存储在39个不同的MD模拟轨迹中获得的DNA的构象细节，包括所有136个独特的四核苷酸步骤。文中还列举了使用这些数据预测DNA结构的例子。
We report here the release of a web-based tool (MDDNA) to study and model the fine structural details of DNA on the basis of data extracted from a set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of DNA. Functionality is included to build all atom models of any user-defined sequence based on the MD results. The backend of this interface is a relational database storing the conformational details of DNA obtained in 39 different MD simulation trajectories comprising all the 136 unique tetranucleotide steps. Examples of the use of this data to predict DNA structures are included.