Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

136

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

Institute of Medical Physics and Biophysics, Leipzig, Germany,

San Diego Supercomputer

Center, San Diego, CA, USA,

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