Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

99-POS Board 19 MDsrv: Viewing and Sharing Molecular Dynamics Simulations on the Web Alexander S. Rose 2,3 , Johanna K. Tiemann 1,3 , Peter W. Hildebrand 1,3 . 1 Institute of Medical Physics and Biophysics, Leipzig, Germany, 2 San Diego Supercomputer Center, San Diego, CA, USA, 3 Institute of Medical Physics and Biophysics, Berlin, Germany. Molecular dynamics (MD) simulations are these days an established and widely used tool to investigate the time resolved motions of biological macromolecules. Sharing of the resulting coordinate trajectories for visualization is complicated by their size, the requirement of having special software set-up and the knowledge of the software usage. However, as research groups and collaborations become increasingly interdisciplinary, it is desirable to make sharing of MD trajectories easier to facilitate discussions and further analyses. In contribution, we present MDsrv, a tool to serve trajectories of molecular coordinates and visualize them in a web browser by employing the NGL Viewer [1]. It supports trajectories formats from different MD software including xtc/trr (GROMACS), nc/netcdf (AMBER) or dcd (NAMD) files. The trajectories can be served within a local network to co-workers or over the Internet to colleagues all over the world. For interactive viewing of the MD simulations only a web browser is needed and no installation of any MD-specific software is required. The trajectories and the NGL Viewer web application are served by a Python module readily installable from PyPI that can be run locally or deployed to a web-server. Together, the client and the server component make data from MD simulations accessible to a wide audience of researchers and students. MDsrv promotes concepts for publishing MD data along with publications of their analysis similar to classical structural biology data published in the PDB. References: [1] Rose, A. S., Hildebrand, P. W., NGL Viewer: a web application for molecular visualization. 2015. Nucleic Acids Res. 2015. 43(W1):W576-9

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