For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
22
views
20
references
 Top references
cited by
194
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      0
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: not found

      NGL viewer: web-based molecular graphics for large complexes

      research-article

      Read this article at

      ScienceOpenPublisherPMC
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Motivation

          The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size.

          Results

          We have tackled this problem by developing highly memory-efficient and scalable extensions for the NGL WebGL-based molecular viewer and by using Macromolecular Transmission Format (MMTF), a binary and compressed MMTF. These enable NGL to download and render molecular complexes with millions of atoms interactively on desktop computers and smartphones alike, making it a tool of choice for web-based molecular visualization in research and education.

          Availability and implementation

          The source code is freely available under the MIT license at github.com/arose/ngl and distributed on NPM (npmjs.com/package/ngl). MMTF-JavaScript encoders and decoders are available at github.com/rcsb/mmtf-javascript.

          Related collections

          Most cited references20

          • Record: found
          • Abstract: found
          • Article: not found

          The Protein Data Bank.

          H M Berman, J Westbrook, Z. Feng … (2000)
          The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
          Article 0 comments Cited 3669 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            The RCSB protein data bank: integrative view of protein, gene and 3D structural information

            Peter W Rose, Andreas Prlić, Ali Altunkaya … (2016)
            The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.
            Article 0 comments Cited 293 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              NGL Viewer: a web application for molecular visualization

              Alexander Rose, Peter W. Hildebrand (2015)
              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.
              Article 0 comments Cited 165 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                Alfonso Valencia: Role: Associate Editor
                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (iso-abbrev): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 01 November 2018
                Publication date (Electronic): 29 May 2018
                Publication date PMC-release: 01 November 2019
                Volume: 34
                Issue: 21
                Pages: 3755-3758
                Affiliations
                [1 ]RCSB Protein Data Bank
                [2 ]San Diego Supercomputer Center, UC San Diego, CA, USA
                Author notes
                To whom correspondence should be addressed. E-mail: asr.moin@ 123456gmail.com
                Author information
                http://orcid.org/0000-0002-0893-5551
                http://orcid.org/0000-0003-1018-5718
                http://orcid.org/0000-0001-9981-9750
                Article
                Accession ID: PMC6198858 Pmcid ID: PMC6198858 Pmc-uid ID: 6198858 Publisher ID: bty419
                DOI: 10.1093/bioinformatics/bty419
                PMC ID: 6198858
                PubMed ID: 29850778
                SO-VID: bed5c345-8109-4ca2-94d1-eec6fada7b9d
                Copyright © © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com
                License:

                This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model ( https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

                History
                Date received : 15 August 2017
                Date revision received : 04 May 2018
                Date accepted : 22 May 2018
                Page count
                Pages: 4
                Funding
                Funded by: NIH 10.13039/100000002
                Award ID: U01 CA198942
                Funded by: RCSB
                Funded by: PDB
                Funded by: NSF 10.13039/100000001
                Funded by: NIH 10.13039/100000002
                Funded by: NSF 10.13039/100000001
                Award ID: DBI-1338415
                Categories
                Subject: Applications Notes
                Subject: Structural Bioinformatics

                Data availability:

                Comments

                Comment on this article