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.

1. INTRODUCTION
As in situ observation of structural properties and physicoche-
mical 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 visua-
lizers. 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.
Regarding pure visualization features, BiovizJS brings cutting
edge WebGL rendering effects:
Impostors rendering2
(*) for representations in volving 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.
BiovizJS: a versatile 3D molecular visualizer
anywhere, anytime and with any device
/RESOURCE
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.
Fig.1: Yeast 80S ribosome (4V7R) visualization with impostors. Enabling to view and interact with large structures in real time.
© BIONEXT 2017. Technology developed in Strasbourg, France. Bionext may be registered trademarks or service marks of Bionext registered in many jurisdictions worldwide. This document is
current as of the initial date of publication and may be changed by Bionext at any time.
https://biosight.bionext.com
01
3D
Visualization
Embedded
Animation
scripting
« BiovizJS is integrated into
the Biosight platform and
NextProt.

2. 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;
Animageexporttoolwithatransparentbackgroundsupport,
making it easier to integrate our visual representations to
your publications and scientific communications.
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 ex-
periences, 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 browser3
.
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 BioSight4
and by NextProt5
, 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.
REFERENCES
1. https://threejs.org/
2. Sigg C. et al. (2006) GPU-based ray-casting of quadratic surfaces. In: Botsch
M, Chen B, Pauly M, Zwicker M, editors. Symp. Point-Based Graph. Aire-la-Ville:
The Eurographics Association; pp. 59–65
3. http://caniuse.com/#search=webgl
4. https://biosight.bionext.com
5. https://www.nextprot.org
(*) : Depending on your graphics configuration compatibility
Fig.2: Highligting clomipramine in crystal structure of LeuBAT (4MMA).
Fig.3: Binding cavities using molecular surface representation.
Fig.4: WebGL compatibility chart.
© BIONEXT 2017. Technology developed in Strasbourg, France. Bionext may be registered trademarks or service marks of Bionext registered in many jurisdictions worldwide. This document is
current as of the initial date of publication and may be changed by Bionext at any time.
https://biosight.bionext.com
ABOUT BIONEXT
BIONEXTisaFrenchbioinformaticscompanyfounded
in 2009 and dedicated to the better understanding
and treatment of various diseases. As such, BIONEXT
focuses on pharmaceutical problematics with a ma-
jor interest in guiding the prediction of biochemical
compounds for pharmaceuticals targets. BIONEXT
aims to accelerate and improve the effectiveness
of drug development and biological research by
developing programs and software-based tools to
tackle problematics of prime importance in the phar-
maceutical field, such as drug profile assessment or
suggestion of drug repurposing. Our first application
BioBind is based on the now accepted principle
that similar receptors bind similar ligands.
www.bionext.com
02
3D
Visualization
Embedded
Animation
scripting