Tag: NCBI Structure

Structure viewer iCn3D version 3 featuring analysis of 3D structures!

The NCBI structure viewer iCn3D version 3 is now available on the NCBI web site and from GitHub.

Analysis of 3D Structures

You can use the current version with the icn3d package at npm to write scripts to call functions in iCn3D. For example, this script on GitHub can calculate the change in interactions due to a mutation.  The results of this analysis for the structure (6M0J) of the SARS-CoV-2 spike protein bound to the ACE2 receptor are displayed in Figure 1. These show the predicted changes in interactions with other residues in the the SARS-CoV-2 spike protein and in the ACE2 receptor when the asparagine (N) at position 501 of the spike protein is changed to a tyrosine (Y). You can also run these scripts from the command line to process a list of 3D structures to get and analyze annotations.

Figure 1. iCn3D viewer showing the predicted interactions with other residues in the spike protein and in the ACE2 target when the asparagine (N) at position 501 of the SARS-CoV-2 spike protein is substituted with  tyrosine (Y), highlighted in yellow. Interactions were calculated using the script interactions2.js.

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New viral protein domain models for annotation of coronaviruses

NLM’s Conserved Domain Database (CDD) has expanded its scope to now include 153 new viral protein domain family models for the annotation of coronaviruses, including models such as for the S1 subunit of coronavirus Spike proteins (cd21527), the nucleocapsid (N) protein of coronavirus (cd21595), and the coronavirus RNA-dependent RNA polymerase (cd21530).

Each curated domain model consists of a multiple sequence alignment containing conserved sequence features that may have been confirmed experimentally, plus links to relevant publications. When available, the domain models include 3D structures with links to interactive 3D views and interacting partners.

Check out this tabular summary of SARS-CoV-2 gene products for links to matching conserved domain models and representative 3D protein structures.

Want to view these alignments in 3D space? We’ve updated iCn3D, a web-based 3D structure viewer, with new rendering, annotation, and alignment features.  Read more about how you can use iCn3D to view and analyze SARS-CoV-2-related structures.

Don’t forget to review our SARS-CoV-2 resources page to keep up to date on other coronavirus data at NCBI!

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

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.

Continue reading “Conserved Domain Database (CDD) v. 3.18 is now available”

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.