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. 2020 Jan 1;36(1):131-135.
doi: 10.1093/bioinformatics/btz502.

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

Jiyao Wang  1 , Philippe Youkharibache  1   2 , Dachuan Zhang  1 , Christopher J Lanczycki  1 , Renata C Geer  1 , Thomas Madej  1   2 , Lon Phan  1 , Minghong Ward  1 , Shennan Lu  1 , Gabriele H Marchler  1 , Yanli Wang  1 , Stephen H Bryant  1 , Lewis Y Geer  1 , Aron Marchler-Bauer  1
Affiliations

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

Jiyao Wang et al. Bioinformatics. .

Abstract

Motivation: Build a web-based 3D molecular structure viewer focusing on interactive structural analysis.

Results: iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure-structure alignments obtained from NCBI's VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1.

Availability and implementation: iCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
iCn3D visualizing the structure of tumor suppressor P53 complexed with DNA (PDB code 1TUP). This display can be reproduced in a live browser window with the shortened sharable link: https://icn3d.page.link/2rZWsy1LZmtTS3kBA. (a) ‘iCn3D PNG Image’ saved using the option ‘Save File’ in the File menu. (b) A list of defined sets including chains and custom sets (top), and a 2D schematic of the molecules involved in the complex structure (bottom). (c) Summary view of sequences and annotations with residues represented as vertical bars. (d) Detailed view of sequences and annotations
Fig. 2.
Fig. 2.
iCn3D visualizing the sequence alignment of protein accession NP_001108451.1 with structure accession 1TSR_A (chain A of 3D structure 1TSR). The alignment is shown in the box around ‘Protein 1TSR_A’ in the sequence window. (Share Link: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html? from=icn3d&blast_rep_id=1TSR_A&query_id=NP_001108451.1)
Fig. 3.
Fig. 3.
iCn3D visualizing the structure superposition and corresponding alignments between human oxy and deoxyhemoglobin (PDB ID 1HHO and 4N7N), as computed by VAST+. (Share Link: https://icn3d.page.link/wPoW56e8QnzVfuZw6)
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References

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