2021
DOI: 10.1101/2021.09.10.459868
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iCn3D: From Web-based 3D Viewer to Structural Analysis Tool in Batch Mode

Abstract: iCn3D was originally released as a web-based 3D viewer, which allows users to create a custom view in a life-long, shortened URL to share with colleagues. Recently, iCn3D was converted to use JavaScript classes and could be used as a library to write Node.js scripts. Any interactive features in iCn3D can be converted to Node.js scripts to run in batch mode for a large data set. Currently the following Node.js script examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode: ligand-protein i… Show more

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Cited by 5 publications
(5 citation statements)
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“…Given the rapidly changing landscape of the SARS-CoV-2 virus and the frequent emergence of variants of concern (VOCs), the ability to identify which mutations in the VOCs are likely to impact antigen-binding properties of a specific antibody is a desired feature. To provide a visual interpretation template, we incorporated a 3D visualization tool, iCn3D ( 4 ), in the main page of the database website. By clicking on a COVIC-ID in the summary table ( Figure 2C ), the color-coded epitope footprint, as defined from negative stain electron microscopy studies ( 1 ) or predicted from high-resolution epitope binning corresponding to the highlighted antibody epitope is displayed on the structure of the Spike protein ( Supplementary Figure S2 ).…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…Given the rapidly changing landscape of the SARS-CoV-2 virus and the frequent emergence of variants of concern (VOCs), the ability to identify which mutations in the VOCs are likely to impact antigen-binding properties of a specific antibody is a desired feature. To provide a visual interpretation template, we incorporated a 3D visualization tool, iCn3D ( 4 ), in the main page of the database website. By clicking on a COVIC-ID in the summary table ( Figure 2C ), the color-coded epitope footprint, as defined from negative stain electron microscopy studies ( 1 ) or predicted from high-resolution epitope binning corresponding to the highlighted antibody epitope is displayed on the structure of the Spike protein ( Supplementary Figure S2 ).…”
Section: Resultsmentioning
confidence: 99%
“…The database utilizes a PostgreSQL relational database management system with the application backend implemented as a Django web framework and the frontend/user interface built using D3.js and Angular. The 3D viewer tool for visualizing the epitope footprints on Spike is implemented using iCn3D, a structure viewer written in JavaScript ( 4 ).…”
Section: Methodsmentioning
confidence: 99%
“…Structure models with the highest average predicted Local Distance Difference Test (pLDDT) scores (Model 1) were selected for structure images by exporting PDB files. 3-D structure images were generated using iCn3D (Wang, et al 2020; Wang, et al 2022) (https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html).…”
Section: Methodsmentioning
confidence: 99%
“…The highest confidence 3D model of each protein prediction was submitted to VAST Search (https://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html) (22), which compares the 3D coordinates of a submitted protein structure (including those modeled by AlphaFold) to all solved 3D structures in NCBI's Molecular Modeling Database, to help identify structure neighbors of interest. 3D visualization was performed using iCn3D for most proteins (23,24), while the structural alignment and overlay visualization of SaoP with the MetI dimer used ChimeraX (25).…”
Section: Structure Predictionmentioning
confidence: 99%