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MDsrv: viewing and sharing molecular dynamics simulations on the web

Nature Methods volume 14, pages 1123–1124 (2017)Cite this article

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To the Editor:

Molecular dynamics (MD) simulations are a well-established technique to investigate time-resolved motions of biological macromolecules at atomic resolution1. Methodological advances, continued software optimization and hardware acceleration have broadened the applicability of MD simulations with respect to feasible system size, runtime and quality2. Coupled to these advances, availability of vast cloud storage is enabling the creation of MD trajectory databases3. However, accessing, viewing and sharing MD trajectories is restricted by large file sizes and the need for specialized software (e.g., VMD, Chimera, Schrodinger Suite Products), which greatly limits the audience to which the MD data are available. In light of increasingly interdisciplinary research and remote collaborations, it is desirable to make the atom trajectories of MD simulations widely available to facilitate interactive exploration and collaborative visual analysis as well as to promote discussions. While some tools exist for analysis or visualization of trajectories, none of these offers a straightforward and easy solution for sharing and viewing MD trajectories online (for a comparison, see Supplementary Note 1).

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Figure 1: Schematic display of MDsrv's capabilities.

References

  1. Levitt, M. Angew. Chem. Int. Edn. Engl. 53, 10006–10018 (2014).

    Article  CAS  Google Scholar 

  2. Dror, R.O., Dirks, R.M., Grossman, J.P., Xu, H. & Shaw, D.E. Annu. Rev. Biophys. 41, 429–452 (2012).

    Article  CAS  Google Scholar 

  3. Doerr, A. Nat. Methods 7, 426 (2010).

    Article  CAS  Google Scholar 

  4. Rose, A.S. & Hildebrand, P.W. Nucleic Acids Res. 43, W576–W579 (2015).

    Article  CAS  Google Scholar 

  5. Guixà-González, R. et al. Nat. Commun. 8, 14505 (2017).

    Article  Google Scholar 

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Acknowledgements

This project was supported in part by RCSB PDB, which is jointly funded by the NSF, the NIH, and the US DoE (NSF DBI-1338415; PI, S.K. Burley), Deutsche Forschungsgemeinschaft (Sfb740/B6, DFG HI 1502/1-2, BI 893/8 all to P.W.H.), Berlin Institute of Health (to P.W.H.), and funds by Stiftung Charité (to P.W.H.). Computing resources for the simulation sessions were in part provided by Norddeutscher Verbund für Hoch und Höchstleistungsrechner (to P.W.H.).

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Authors and Affiliations

  1. Institute of Medical Physics and Biophysics, Charité University Medicine, Berlin, Germany

    Johanna K S Tiemann, Ramon Guixà-González, Peter W Hildebrand & Alexander S Rose

  2. Institute of Medical Physics and Biophysics, University Leipzig, Leipzig, Germany

    Johanna K S Tiemann & Peter W Hildebrand

  3. RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, USA

    Alexander S Rose

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  1. Johanna K S Tiemann
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  2. Ramon Guixà-González
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  3. Peter W Hildebrand
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  4. Alexander S Rose
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Corresponding authors

Correspondence to Peter W Hildebrand or Alexander S Rose.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 MDsrv command-line usage and NGL scripting example.

(A) Command-line usage of the 'mdsrv' tool. To open and view a MD trajectory in a browser, a structure and a trajectory file must be supplied. Optionally, a script file can be loaded to automate creation of complex molecular scenes (see B). Further arguments allow basic server configuration, such as setting port or host. (B) Example NGL script. The JavaScript-based code loads the md.gro structure file and adds the md.xtc trajectory to it. Display is limited to non-hydrogen protein atoms. A cartoon and a licorice representation are added. Finally the view is centered.

Supplementary Figure 2 Example how to present simulations embedded into a website.

Supplementary Figure 3 Graphical user interface (GUI) of the MDsrv web application.

(A) The main GUI. The sidebar on the right shows loaded files and added representations in collapsible panels with sub-elements including atom selection/filter (funnel symbol), trajectory (disk stack symbol) or menu (stacked bars symbol). The menu bar at the top provides access to general options. (B) By selecting 'File', (C) a submenu pops up from where structure files or NGL scripts can be loaded. (D) Trajectories can be loaded from the structure menu. (E) A “Remote Trajectory” is streamed by MDsrv whereas (E) a “Trajectory” import loads a file all at once. (F) Within the trajectory menu are options for handling superposition and periodic boundary conditions as well as playback settings. (G) By picking an atom or bond in any representation, their information is shown in the lower left of the GUI.

Supplementary Figure 4 Snapshots of MD simulations viewed with MDsrv.

(A) Self-assembly of three Bace1 transmembrane helices in a DPPC lipid bilayer obtained from coarse-grained MD simulations with carbons in grey, polar lipid head groups in red balls and water molecules in blue balls. (B) Cholesterol (green or grey hyperballs) enters the A2A receptor (violet cartoon) during MD simulations performed in a mixed lipid bilayer with carbons in grey, oxygens in red and nitrogens in blue19. (C) Simulations of a huge complex containing more than 550,000 atoms. The Gs protein (pink) is bound to the beta2 adrenoceptor (violet) within a phospholipid bilayer solvated in water (color code as in B, hydrogens in white) (D) Decisive differences in hydrogen bonding comparing bovine (yellow) with human rhodopsin20.

Supplementary information

Supplementary Figures and Text

Supplementary Figures 1–4, Supplementary Notes 1–4 and Supplementary Table 1 (PDF 17225 kb)

Life Sciences Reporting Summary

Life Sciences Reporting Summary (PDF 66 kb)

Supplementary Software 1

Mdsrv-0.3.5.tar.gz (Python package containing the source code of Mdsrv, installable with pip or easy_install) (ZIP 746 kb)

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Tiemann, J., Guixà-González, R., Hildebrand, P. et al. MDsrv: viewing and sharing molecular dynamics simulations on the web. Nat Methods 14, 1123–1124 (2017). https://doi.org/10.1038/nmeth.4497

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