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      NGL Viewer: a web application for molecular visualization

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      * ,
      Nucleic Acids Research
      Oxford University Press

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          Abstract

          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.

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          Most cited references20

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          The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

          The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.
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            3Dmol.js: molecular visualization with WebGL

            Summary: 3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. Availability and implementation: 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu Contact: dkoes@pitt.edu
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              Jmol– a paradigm shift in crystallographic visualization

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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                01 July 2015
                29 April 2015
                29 April 2015
                : 43
                : Web Server issue
                : W576-W579
                Affiliations
                Institut für Medizinische Physik und Biophysik, AG ProteInformatics, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +49 030 450524170; Fax: +49 030 450524952; Email: alexander.rose@ 123456charite.de
                Article
                10.1093/nar/gkv402
                4489237
                25925569
                9b5da837-3f2f-4607-a805-5173830004b1
                © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 15 April 2015
                : 11 April 2015
                : 05 March 2015
                Page count
                Pages: 4
                Categories
                Web Server issue
                Custom metadata
                1 July 2015

                Genetics
                Genetics

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