MDsrv: visual sharing and analysis of molecular dynamics simulations. Issue Volume 50:Issue W1(2022) (26th May 2022)

• Record Type: Journal Article
• Authors: Kampfrath, Michelle; Staritzbichler, René; Hernández, Guillermo Pérez; Rose, Alexander S; Tiemann, Johanna K S; Scheuermann, Gerik; Wiegreffe, Daniel; Hildebrand, Peter W
• Is Part Of: Nucleic acids research. Volume 50:Issue W1(2022)
• Page Start: W483
• Page End: W489
• Publication Date: 2022-05-26
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac398
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: 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. Graphical Abstract: