NGL viewer: web‐based molecular graphics for large complexes

By Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose. 2018

446 citations recorded by the source corpus.

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.

Subfields: Computer Graphics and Computer-Aided Design, Computer Vision and Pattern Recognition, Physical and Theoretical Chemistry

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Jose M. Duarte

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Citations in the corpus

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit (2020, methodology): “In the resulting view, the modeled structure is displayed in the NGL Viewer application (Rose et al., 2018) for molecular visualization, and an option is also provided to download the atomic coordinates (Fig.”
BERTology Meets Biology: Interpreting Attention in Protein Language Models (2020, methodology): “Visualizations based on the NGL Viewer [54, 67, 68]. seeks to shed light on biological processes that are not yet fully understood.”
DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations (2020, methodology): “All interatomic contacts calculated with Arpeggio are also displayed as an interactive viewer using NGL viewer.(53) On the “Mutation List” option, the results are displayed as a downloadable table with options to view details of each variation separately, similarly to the analysis provided by the “S”
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics (2020, methodology): “This allows the end-user to either use tools made available in the NGL Viewer instance to interrogate the simulation or to download the data for offline processing.”
RCSB Protein Data Bank: Enabling biomedical research and drug discovery (2019, unknown): “Rapid 3D visualization of structures large and small is possible using the NGL viewer, 20 which includes specialized options for viewing ligand interactions and electron density maps.”
Fast and accurate protein structure search with Foldseek (2022, methodology): “We implemented a structural visualization using the NGL viewer 44 to aid the investigation of pairwise hits.”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update (2022, methodology): “org/learn/visualization/charts/), as well as more specialized visualization tools such as Cytoscape (3), NGL molecular visualizations (4), and geographic maps from OpenLayers.”
SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina (2024, methodology): “The 3D structure of the target protein and the calculated poses of the ligand are displayed on the submission and result pages, respectively, with the NGL Viewer (version 2.1.0) in JavaScript ( 41 ).”
mCSM-PPI2: predicting the effects of mutations on protein–protein interactions (2019, methodology): “For the Single Mutation option (Supplementary Figure S3), mCSM-PPI2 outputs the predicted change in binding affinity (in kcal / mol) along with an interactive 3D viewer, built using NGL viewer (51), showing non-covalent interactions, generated with Arpeggio, at the mutated position.”
The HDOCK server for integrated protein–protein docking (2020, background): “However, it should be noted that the accuracy of 3D structures generated by homology modeling is strongly dependent on the sequence identity between target and template 36 , although our docking strategy and scoring function can consider some degree of structural uncertainties.”
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures (2019, methodology): “The structure of the domain is visualized using NGL viewer (17) and displayed within the context of a given PDB entry.”
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy (2018, methodology): “org also offer fast, interactive 3D display of molecular complexes containing millions of atoms on desktop computers (without any special plug-ins) and even smartphones and tablets using the NGL Viewer [Figure 4, (40,41)].”