The NCBI Structure Group
What's New
   3D Macromolecular Structures   Conserved Domains   PubChem   BioSystems 
  3D Macromolecular Structures back to top  

[17 December 2018]  iCn3D 2.4.0 is now available on NCBI web servers and from GitHub ( As an example of the updated web application, open the structure for 1TUP: Tumor Suppressor P53 Complexed With Dna on the web, or use iCn3D's "File" menu to retrieve a structure by its ID or to open a structure file on your local computer. An iCn3D Web APIs document describes how to use the iCn3D structure viewer in your own web page.

New features in this release include:

  • An option to display an electron density map for any subset of a crystal structure is now available from the iCn3D "Style" menu.
  • The iCn3D PNG image file, which is generated by the "File > Save Files > iCn3D PNG Image" menu option, now includes both a static image of the structure and a URL that captures the series of iCn3D commands (e.g., selections, styles, colors, position) that were used to customize the structure before it was saved. As a result, the PNG file can either be viewed as a static image (if opened in photo viewing software), or as an interactive 3D structure (if opened in iCn3D using the "File > Open File > iCn3D PNG Image" menu option). The URL that is saved as part of the iCn3D PNG Image file is the same as the URL produced by iCn3D's "File > Share Link" menu option.
  • Gene symbols are now displayed in the "Sequences and Annotations" window.
  • The Change Log section of the iCn3D Web API help document lists additional enhancements that have been made to iCn3D since the release of iCn3D 2.0 in April 2018.

[27 JULY 2016]  New version of VAST+ featuring refined 3D alignments.  A new version of VAST+ was released. It provides a refined structure-based alignment of similar macromolecular complexes, and displays the 3D superpositions in the recently released iCn3D, a WebGL-based structure viewer. The initial alignment of similar macromolecular complexes, which became available with the first release of VAST+, uses the complete set of individually aligned macromolecules and corresponding matching amino acids to calculate a superposition of the complex structures. In contrast, the new release of VAST+ identifies a subset set of amino acids that have highly similar 3D positions in the query and subject complex structure, and uses it to create a refined alignment that allows identification and visualization of the most similar portion of the structures (the structurally invariant core of the assembly), as well as the differences between the structures.

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  Conserved Domains and Protein Classification back to top  

[29 MAR 2017]  A new version of the Conserved Domain Database (CDD) has been released. Version 3.16 contains 1,659 new or updated NCBI-curated domains, including models specifically built to annotate structural motifs (accession prefix "sd"), and now mirrors Pfam version 30. A fine-grained classification of the 7-membrane GPCR transmembrane subunit has been added. In addition, the default database size parameters for CD-Search has been adjusted, resulting in slightly higher E-values. Fewer models are now assigned a multi-domain-model status, affecting the domain annotation of a large number of proteins. You can access CDD from and find updated content on the CDD FTP site at Database statistics, showing the number of domain models from each source database, are provided on the CDD News page.

[12 OCT 2016]  The Subfamily Protein Architecture Labeling Engine (SPARCLE) is now available. It is a resource for the functional characterization and labeling of protein sequences that have been grouped by their characteristic domain architecture. To use SPARCLE, you can either: (1) enter a query protein sequence into CD-Search, which will display a "Protein Classification" on the results page if the query protein has a hit to a curated domain architecture in the SPARCLE database, or (2) search the SPARCLE database by keyword to retrieve domain architectures that contain the term(s) of interest in their descriptions. With either approach, the corresponding SPARCLE record(s) will display the name and functional label of the architecture, supporting evidence, and links to other proteins with the same architecture. Additional information and illustrated examples are provided on the "About SPARCLE" page.

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  PubChem back to top  

[21 MAR 2017]  On April 2-6, 2017, the 253rd American Chemical Society National Meeting will be held in San Francisco, CA. The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. To learn more about this, please read this post.

[29 NOV 2016]  PubChem now uses the latest IUPAC recommendations for atomic mass and isotopic composition information. In addition, the allowed isotopes for a given element are restricted to those with a half-life of one millisecond or greater. These changes affect the molecular weight values computed for nearly all compounds in PubChem. To learn more, please read this post.

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  BioSystems back to top  

[21 OCT 2011]  The Gene Ontology (GO) is now available in the BioSystems database. GO is an initiative to standardize the representation of gene and gene product attributes across species and databases and provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data. The BioSystems database links GO records to associated genes and proteins. The BioSystems help document describes how the links are made and provides more details about the source databases.

Retrieve all GO records from the NCBI BioSystems database, or only the records from the following categories:

- biological processes (root record)
- cellular components (root record)
- molecular functions (root record)

If you open the root record for any category, you can use the "Related BioSystems:Subset BioSystems" folder tab to view the nodes beneath it. The other GO records will also have "Subset and/or Superset BioSystems" folder tabs, allowing you to browse up and down the GO hierarchy and to retrieve the associated genes and proteins, as available, for any node.

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Revised 19 December 2018