NGL Viewer: a web application for molecular visualization.

Alexander S Rose,Peter W Hildebrand

doi:10.1093/nar/gkv402

Alexander S Rose, Peter W Hildebrand

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https://doi.org/10.1093/nar/gkv402

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Journal: Nucleic Acids Research	Publication Date: Apr 29, 2015
Citations: 401	License type: CC BY 4.0

Affiliation: Charité - Universitätsmedizin Berlin

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The NGL Viewer (http://proteinformatics.charite.de/ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data. It supports common structural file-formats (e.g. PDB, mmCIF) and a variety of molecular representations (e.g. ‘cartoon, spacefill, licorice’). Moreover, the viewer can be embedded in other web sites to provide specialized visualizations of entries in structural databases or results of structure-related calculations.

Highlights

Visualizing 3D molecular structures of biopolymers has become a common task in the life sciences [1,2]
Fast 3D graphics are enabled by graphics processor unit (GPU) acceleration available through WebGL, a standard based on the OpenGL ES 2.0 application programming interface (API) and built directly into the browser without the need for any plug-ins
The source code is organized into task-specific modules: parsing and processing of molecular structures; transforming molecular structures into display representations such as spheres for atoms, sticks for bonds or tubes tracing a protein backbone; rendering of display representations on the GPU with WebGL; and, creating an interactive graphical user interface (GUI)

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Visualizing 3D molecular structures of biopolymers has become a common task in the life sciences [1,2]. The NGL Viewer (http://proteinformatics.charite.de/ ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is unaffected by the retirement of third-party plug-ins like Flash and Java Applets.

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