iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures

Abstract

SummaryiCn3D (I-see-in-3D) is a web-based 3D molecular structure viewer focusing on the interactive structural analysis. It 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 alignment 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 implementationiCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d.Supplementary informationUser instructions are available at Bioinformatics online

A Novel Protein from Ectocarpus sp. Improves Salinity and High Temperature Stress Tolerance in Arabidopsis thaliana

“…As the model generated by SWISS-MODEL covered only the DUF1768-domain, another tertiary structure homology-modelling was carried out using DMPfold [ 51 ]. The PDB files generated by ProMod3 v. 3.0.0 and DMPfold were visualized using iCn3D [ 52 ].…”

Topological and Structural Plasticity of the single Ig fold and the double Ig fold present in CD19

“…Methods have been published previously (Youkharibache 2019). Software Programs used in this work are iCn3D (J. Wang et al 2020), CEsymm (Myers-Turnbull et al 2014), SYMD (Tai et al 2014) that has been integrated recently to iCn3D as a web service, Cn3D for interactive multiple structure alignment (Y.…”

“…This is visualized in Figure 2 and beyond through the coloring scheme we have chosen to highlight symmetry with protodomain equivalence. (3D pictures are either from Chimera (Pettersen et al 2004) or iCn3D (J. Wang et al 2020).…”

Molecularly imprinted polymers by epitope imprinting: a journey from molecular interactions to the available bioinformatics resources to scout for epitope templates

“…In particular, iCn3D is a WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures and chemicals on the Web that does not require installing a separate application. It can be accessed from the "molecular graphic" that appears on the structure summary page for any record in the Molecular Modeling Database (MMDB) [94]. The topological information related to the protein are linked out to databases that store experimental evidence over the proteinprotein interaction areas, links to literature metadata, and predicted information gathered by any available protein-protein interaction databases (see for example: http://string-db.org; https://www.ebi.ac.uk/intact/), providing a panel of criteria for the selection of a one final epitope sequence.…”