Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany.
Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.
Nucleic Acids Res. 2022 Jul 5;50(W1):W483-W489. doi: 10.1093/nar/gkac398.
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration and collaborative visual analysis. We have now enhanced the MDsrv to further simplify the upload and sharing of MD trajectories and improve their online viewing and analysis. With the new instance, the MDsrv simplifies the creation of sessions, which allows the exchange of MD trajectories with preset representations and perspectives. An important innovation is that the MDsrv can now access and visualize trajectories from remote datasets, which greatly expands its applicability and use, as the data no longer needs to be accessible on a local server. In addition, initial analyses such as sequence or structure alignments, distance measurements, or RMSD calculations have been implemented, which optionally support visual analysis. Finally, based on Mol*, MDsrv now provides faster and more efficient visualization of even large trajectories compared to its predecessor tool NGL.
分子动力学模拟是一种经过验证的技术，可用于计算和可视化大分子在原子分辨率下的时间分辨运动。MDsrv 是一种工具，可流式传输 MD 轨迹，并在网络浏览器中进行交互式显示，而无需高级技能，从而促进交互式探索和协作式可视化分析。我们现在已经增强了 MDsrv，以进一步简化 MD 轨迹的上传和共享，并改进其在线查看和分析。有了新的实例，MDsrv 简化了会话的创建，这允许使用预设表示和视角来交换 MD 轨迹。一项重要的创新是，MDsrv 现在可以访问和可视化来自远程数据集的轨迹，这大大扩展了它的适用性和用途，因为数据不再需要在本地服务器上访问。此外，已经实现了初始分析，例如序列或结构比对、距离测量或 RMSD 计算，这些分析可选地支持视觉分析。最后，与前身工具 NGL 相比，基于 Mol*，MDsrv 现在可以更快、更有效地可视化即使是大型轨迹。
