NGL viewer: web-based molecular graphics for large complexes
Open accessAbstract
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.
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The 3D visualization employs NGL Viewer and is highly interactive, allowing users to drag, zoom, pan and spin the structure to thoroughly examine it.
“This 3D visualization, employing NGL Viewer (34,35), is highly interactive, allowing users to drag, zoom, pan and spin the structure to thoroughly examine it.”
From TCRD and pharos 2021: mining the human proteome for disease biology (2021) · cites this paper as [34]
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- Authors
- Rose, A. S., Bradley, A. R., Valasatava, Y., Duarte, J. M., Prlić, A., & Rose, P. W.
- Affiliations
- San Diego Supercomputer Center (US)
- RCSB Protein Data Bank
- Corresponding author
- Rose, Alexander S
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-05-29
- Volume
- 34
- Issue
- 21
- Pages
- 3755-3758
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC6198858
- OpenAlex
- W2806399642
- Cited by
- 489
- References
- 19
- Citations by year
- 2026: 21 · 2025: 33 · 2024: 45 · 2023: 45 · 2022: 50 · 2021: 79 · 2020: 108 · 2019: 96 · 2018: 11 · 2016: 1
- FWCI
- 27.53
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- NIH (U01 CA198942)
- RCSB
- PDB
- NSF (DBI-1338415)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computer Graphics and Computer-Aided Design › Computer Graphics and Visualization Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- molecular visualization, macromolecular complexes, WebGL, memory-efficient rendering, web-based visualization, interactive rendering, mobile devices
- MeSH terms
- Computer Graphics, Software, Internet, Macromolecular Substances
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