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

[17 August 2016]  iCn3D 2.0 is now available on NCBI web servers ( and on GitHub ( New features in this release include:

  • an interactions schematic (2D view) that is available when a structure is loaded as an MMDB file. It can be used to select/highlight molecular components (illustrated example) or interaction interfaces (illustrated example)
  • calculation of secondary structures if the input PDB file does not define secondary structure information
  • previous files src/icn3d.js, src/full_ui.js, and src/simple_ui.js have been separated into small files
The iCn3D help document provides additional details about the viewer, including examples of how iCn3D can be used.

[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.

[28 APRIL 2016]  iCn3D 1.0 is now available.  It is a new WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures on the web, without the need to install a separate application, and enables you to:

  • interactively view 3D structures and corresponding sequence data
  • interactively view superpositions of similar structures
  • cutomize the display of a structure and generate a URL that allows you to share the link
  • incorporate iCn3D into your own pages
An example of each is accessible from the "About iCn3D" page.
iCn3D can be accessed from the molecular graphic that appears on the structure summary page for any record in the Molecular Modeling Database (MMDB).
As an example, view the MMDB summary page for the Tumor Suppressor P53 Complexed with DNA (1TUP). Click on the spin icon in the molecular graphic to open the structure in the basic version of iCn3D, or click on the launch icon icon that launches full feature iCn3D in another window to open the structure in the advanced (full feature) version of iCn3D in a separate window.
You can also access the advanced version of iCn3D directly at, where you can use the "File" menu to retrieve a structure by its ID or to open a structure file on your local computer.
The source code is available from GitHub ( for developers who would like to customize the program and/or contribute code, and for users who would like to run the program on their local computer.

[28 APRIL 2016]  New structure summary pages featuring interactive molecular graphic.  MMDB structure summary pages have been revised to feature interactive molecular graphics using iCn3D, a new WebGL-based viewer for three-dimensional macromolecular structures. A spin icon in the molecular graphic loads a basic version of iCn3D into the web page, enabling you to render the structure in the desired style and highlight molecules of interest by clicking on the corresponding interactions schematic. A launch icon icon that launches full feature iCn3D in another window opens the advanced (full feature) version of iCn3D in a separate window. As an example, view the MMDB summary page for Tumor Suppressor P53 Complexed With DNA (1TUP). Additional information is available in the MMDB help document and the About iCn3D page.

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  Conserved Domains and Protein Classification back to top  

[27 JUN 2016]  A new version of the Conserved Domain Database (CDD) has been released. Version 3.15 contains 290 new or updated NCBI-curated domains, including models specifically built to annotate structural motifs (accession prefix "sd"), and now mirrors Pfam version 28. A fine-grained classification of the beta lactamase-like metallohydrolases has been added. In addition, the default sort order of conserved domain hits in CD Search has been changed, ranking hits by E-value without giving preference to NCBI-curated models. 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.

[30 JUN 2015]  An updated version of the "rpsbproc" command line utility for RPS-BLAST is now available from the CDD FTP site: The output generated by the updated version includes a non-redundant list of structural motifs (accession prefix "sd"), eliminating overlapping structural motifs. Additional information about the "rpsbproc" command line utility is provided in the December 4, 2014 announcement of its initial release.

[20 APR 2015]  The CD-Search service now offers two new options that are designed to improve the consistency of domain annotation, based on known domain architectures. The option to "Rescue Borderline Hits" allows you to see hits that have an E-value above the RPS-BLAST reporting threshold (anywhere between 0.01 and 1.0), and that are consistent with known domain architectures (illustrated example). The option to "Suppress Weak Overlapping Hits" suppresses hits that have an E-value close to the RPS-BLAST reporting threshold (in between 0.01 and 0.001) but overlap with stronger hits (illustrated example). Additional details are provided in a publication by Derbyshire et al., 2015.

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  PubChem back to top  

[17 AUG 2016]  On August 21-25, 2016, the 252nd American Chemical Society National Meeting will be held in Philadelphia, PA. The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. In addition, there will be a Herman Skolnik Award Reception honoring Drs. Stephen Bryant and Evan Bolton for their leadership in the PubChem project. To learn more about this, please read this post.

[03 AUG 2016]  PubChem will adopt a HTTPS-only policy on September 30, 2016. This means PubChem will no longer support HTTP web URLs after that date. The National Center for Biotechnology Information (NCBI) recently announced important changes to NCBI Web Protocols to comply with the US federal government's HTTPS-only policy for all publicly accessible websites. PubChem, as a part of NCBI, will adopt the same HTTPS-only policy. To read more about this, see the PubChem Blog.

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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 18 September 2016