BiovizJS: a versatile 3D molecular visualizer anywhere, anytime and with any device

August 14, 2017

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SUMMARY

Structural properties and physicochemical interactions are of critical interest when studying biomolecules. Therefore, BIONEXT has developed BiovizJS, a 3D molecular visualization Web application runnable on any network connected device. This tool provides both improved and exclusive features for molecular visualization with the aim to enhance your experience in many situations and from any devices. In order to ease its integration into your website, it provides a straightforward API.

INTRODUCTION

As in situ observation of structural properties and physicochemical interactions is critical to have a glimpse of biomolecular mechanisms, three dimensional (3D) visualization tools are main piece of software to structuralists. BiovizJS is the BIONEXT’s 3D molecular visualization Web application built on top of ThreeJS1 , a WebGL graphics library. BiovizJS delivery model allows the user to run it on any network connected device, from desktop computer to handled devices. It offers the same level of functionalities as a native structural visualization tool and is optimized for efficient 3D rendering on major Web browsers. Also, BiovizJS provides a straightforward API, allowing to easily deploy and pilot the application into the user’s website.

MAIN FEATURES

BiovizJS provides most essential features of molecular visualizers. It supports both PDB and PDBX/mmCIF file formats and handles most common molecular representations (e.g. sticks, space fill, cartoon, surfaces…), color mappings (CPK, rainbow, hydrophobicity…) and properties labeling. Besides, BiovizJS includes a measuring tool with two selection profiles and a new representation displaying potential interactions between each molecule chain of the same structure. Finally biological assembly support is available, to study the functional conformational assembly of a molecule.

Yeast 80S ribosome (4V7R) visualization with impostors. Enabling to view and interact with large structures in real time.

Fig. 1

Yeast 80S ribosome (4V7R) visualization with impostors. Enabling to view and interact with large structures in real time.

Regarding pure visualization features, BiovizJS brings cutting edge WebGL rendering effects:

  • Impostors rendering0 for representations involving spheres and/or cylinders like Sticks or Space Fill, enabling large molecules handling such as ribosomes;
  • An advanced transparency management method allowing internal cavities surfaces isolation and visualization(*);
  • A post-processing contours highlighting feature allowing to pinpoint important parts of a molecule with maximal performances;
  • Stereo rendering effect allowing to improve depth perception of molecular arrangements, compatible with both red/cyan glasses and polarized displays.
Highligting clomipramine in crystal structure of LeuBAT (4MMA).

Fig. 2

Highligting clomipramine in crystal structure of LeuBAT (4MMA).

Moreover, BiovizJS offers advanced features to improve your experience:

  • Multimode user control supports regular computer mouses, 3D controllers as well as touch controls, making it usable from any desktop computers and mobile devices such as phones or tablets;
  • An animation scripting language along with a script player, allowing to animate molecules and enliven your scientific presentations. A documentation is available to ease the creation of those scripts;
  • An image export tool with a transparent background support, making it easier to integrate our visual representations to your publications and scientific communications.
Binding cavities using molecular surface representation.

Fig. 3

Binding cavities using molecular surface representation.

Finally, BiovizJS extendable design allows you to embed it according to your needs: feel free to easily enable/disable some help widgets, change default URL of structures repository or enable the script player.

PERFORMANCE & COMPATIBILITY

Unresponsive Web applications prevent friendly user experiences, therefore BiovizJS was designed to be the least invasive on your resources. It also includes a small memory footprint and a low CPU usage, helping to save your battery. Finally BiovizJS is compatible with any WebGL compatible Web browser2.

WebGL compatibility chart.

Fig. 4

WebGL compatibility chart.

CONCLUSION

BiovizJS is an easy to use molecular visualizer developed by BIONEXT and suitable for biomolecular 3D visualizations from any Web browser. Its comprehensive API leverages simple deployment, scripting and modularity to developers. BiovizJS is currently used by our structural analysis platform BioSight3 and by NextProt4, a comprehensive human-centric discovery platform through protein-related data. In summary, BiovizJS provides both improved and exclusive features for molecular visualization with the aim to enhance your experience in many situations from any devices. Feel free to test it at https://biovizjs.bionext.com.

(*) Depending on your graphics configuration compatibility

REFERENCES