Structure viewer iCn3D 2.15.0 with new rendering, annotation, and alignment features

 iCn3D 2.15.0 is now available on NCBI web site and as a release on GitHub. To use the updated web application, retrieve any structure from the Molecular Modeling Database (MMDB), open the structure summary page, and click the button for “full-featured 3D viewer” in the molecular graphic. For example, you can retrieve structures that contain the term SARS-COV-2, click on a structure of interest, then follow the link for “full-featured 3D viewer.” You can also open iCn3D and use the “File” menu to retrieve a structure by its ID, for example 6MOJor to open a structure file from your local computer. spike_protFigure 1. iCn3D showing the structure of the SARS-COV-2 spike protein (6MOJ) with custom coloring of conserved residues and a multiple sequence alignment of other coronavirus spike proteins. The ability to apply custom color to specific residues or chains and the ability to add multiple alignments as tracks are some of the new features available in 2.15.0 Continue reading

Conserved Domain Database (CDD) v. 3.18 is now available

The latest version of the Conserved Domain Database contains 2,128 new or updated NCBI-curated domains and now mirrors Pfam version 32 as well as models from NCBIfams, a collection of protein family hidden Markov models (HMMs) for improving bacterial genome annotation. We have also added fine-grained classifications of the cupin and PBP1 superfamilies. You can find this updated content on the CDD FTP site. Read on for detailed release statistics.

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Publication on NCBI’s web-based structure viewer iCn3D

A recent article by Wang J., et al. describes the features and applications of iCn3D, NCBI’s web-based 3D viewer (Figure 1), and shows how you can use it for interactive structural analysis.

Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, Phan L, Ward M, Lu S, Marchler GH, Wang Y, Bryant SH, Geer LY, Marchler-Bauer A. iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular StructuresBioinformatics. 2019 June 20; pii: btz502. doi: 10.1093/bioinformatics/btz502. (PMID: 31218344

iCN3DFigure 1.  NCBI’s web-based structure viewer iCn3D displaying the TP53 structure 1TUP.

We welcome your input! Please send your suggestions and feedback on the iCn3D viewer to the NCBI Help Desk.