Dixit Surjit B, Beveridge David L
Department of Chemistry and Molecular Biophysics Program Hall-Atwater Laboratories, Wesleyan University, Middletown, CT 06459, USA.
Bioinformatics. 2006 Apr 15;22(8):1007-9. doi: 10.1093/bioinformatics/btl059. Epub 2006 Feb 17.
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.
http://humphry.chem.wesleyan.edu:8080/MDDNA.
Supplementary data including color figures are available at Bioinformatics online.
我们在此报告发布了一个基于网络的工具（MDDNA），用于根据从一组涉及所有独特四核苷酸的DNA序列的分子动力学（MD）轨迹中提取的数据，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序列上下文对DNA的10个独特二核苷酸步的影响。其功能包括根据MD结果构建任何用户定义序列的全原子模型。该界面的后端是一个关系数据库，存储了在39条不同的MD模拟轨迹中获得的DNA构象细节，这些轨迹包含了所有136个独特的四核苷酸步。文中还包括了使用这些数据预测DNA结构的示例。
http://humphry.chem.wesleyan.edu:8080/MDDNA。
包括彩色图表在内的补充数据可在《生物信息学》在线获取。
