Web-based Molecular Graphics

NII Shonan Meeting:

@ Shonan Village Center,September 5-8, 2016


  • Andrea Schafferhans, Technische Universität München, Germany
  • Séan O’Donoghue, CSIRO & Garvan Institute, Australia
  • Haruki Nakamura, Osaka University, Japan


Description of the meeting


Molecular graphics is a well established discipline used in many scientific fields (e.g., life sciences, biomedical research, chemistry, material sciences), including commercial research (e.g., pharmaceutical industry). A wealth of methods and tools have been developed, and are still actively developed – however until recently activity has focused on stand-alone software. This meeting will explore an emerging new frontier for molecular graphics, namely deployment in a server-client environment, which promises to make molecular structural information much more easily accessible to scientists. In addition, the recent hybrid approaches have revealed structures, functions and dynamics of very large molecules and cellular machineries, which are displayed as both atomic structures and molecular/cellular images, greatly extending the roles of molecular graphics. This meeting will bring together key players in this emerging field to explore the challenges and opportunities raised by web-based molecular graphics and new applications.



There is a rapidly growing wealth of molecular structure data that has been derived from experimental methods (e.g., X-ray crystallography, NMR spectroscopy, electron microscopy) and are freely provided from the international database PDB, Protein Data Bank, as well as computational methods, such as molecular dynamics. These data provide scientists today with unprecedented insight into a wide range of molecular phenomena, for example protein function, biological membrane transport, or material properties.

The amount of data is steadily growing in size as well as in complexity: more protein structures, larger protein structures (big complexes) and time-resolved data, such as molecular dynamics trajectories. In the near future, these data may increase in scale to include, for example, complex cellular machineries and whole living cells. A key challenge is to make all of these data accessible to scientists, in ways that enable interpretation and the generation of new research insights.

Fortunately, nowadays almost all scientists – even students – have easy access to computer graphics capabilities powerful enough to show a wide variety of molecular structures. With modern bandwidth speeds, it is even feasible to stream complex, interactive molecular graphics into simple devices such as an iPad or iPhone, via GPU-rendering on a remote server. Thus, it is now possible to depict and explore 3D models in regular browsers, such as Mozilla Firefox, Internet Explorer or Google Chrome. This allows to bring 3D molecular visualisation tools to non-expert end users without the need to install specialised software. However, in times of a steadily growing amount of data, improved visualization methods and tools are urgently needed, which can make the more complex data accessible and interpretable.


Aims of the Seminar

We believe that web molecular graphics is likely to soon become very widely adopted? therefore, we feel it is very timely to host a Shonan meeting on this topic. Overall, we the seminar aims to help give this emerging field direction and clarity, by bringing together global efforts in making molecular structure information available to scientists via the web.

We aim to discuss strategies for effectively managing very large molecular structures (e.g., millions of atoms or more). Most current browsers will fail to visualize these larger molecular structures for various reasons. In some cases (e.g., whole organelles, entire genomes, or materials, such as metal-organic frameworks), the molecular assembly becomes so large that it requires the use of multi-scale, often hierarchical representations that change automatically at different scales, somewhat analogously to Google Maps. Similar strategies can also be needed for large molecular dynamic simulations. All of these cases are a particular challenge for web molecular graphics, which is limited by network bandwidth.

In addition, many of the scientific problems being investigated cannot be solved with molecular graphics alone? instead, data on molecular structures needs to be exchanged with other resources, for example resources that integrate data derived from structures with other information, and display the result using network graphs, or using other visualization paradigms. Therefore, an approach is required which is compatible to different modeling environments. Nowadays, the most widely used scripting language is JavaScript which is moreover used by all recent web browsers. This language seems best suited to be used to interactively combine the website’s content with the molecular 3D visualization via WebGL. The seminar will discuss pros and cons of this architecture and will define desirable interaction paradigms and communication methods.



  1. Common visualization strategies, shader libraries, code bases, and standards for web molecular graphics.
  2. Pros and cons of canvas, WebGL or other approaches.
  3. Native JavaScript versus porting from Java (e.g., JSmol).
  4. Fast web-based visualization of ‘big’ molecular data (e.g., very large molecular structures, molecular dynamics trajectories, massive assemblies such as whole organelles) via efficient transport across the web using data compression. Enabling a user experience with minimum load times.
  5. Re-use and re-deployment, enabling molecular 3D structure data to be easily and reliably accessed by other services (For example, enable protein-protein interaction systems or protein-small molecular systems to get information about molecular interaction surfaces.)
  6. De facto conventions in molecular representation, coloring, layout, and visualization, with the aim of making molecular graphics easier to use and interpret, and to facilitate communication to peers or to the public.
  7. Use of web molecular graphics for new types of educational content? making complex molecular stories more accessible and interactive.
  8. Applications of 3D printing, or immersive stereo graphics to web molecular graphics.
  9. Plans for ongoing engagement of the web molecular graphics community, either via presence in existing international meetings, or possibly creation of a new conference series.
  10. Plans for international collaborative development, projects, and funding schemes that would support global research efforts in the development of web molecular graphics.



In addition to inviting key players in web-based molecular graphics, we will invite members from each of the laboratories behind the main traditional ‘stand-alone’ molecular graphics systems. We would also include prominent scientists that work on applying molecular graphics to the life sciences, biomedicine, chemistry, and material sciences. Furthermore, we will include members of the data visualisation community – especially those interested in web-based graphics? since they have a focus outside of molecular graphics, we expect they will inject ‘out-of-the-box’ thinking, thus helping exploring unconventional, potentially more informative, visualization paradigms.

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