The NCBI Structure Group
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   3D Macromolecular Structures   Conserved Domains   PubChem   BioSystems 

3D Macromolecular Structures

[06 DEC 2013]  VAST+ released! Find 3D structures with similar macromolecular complexes.  VAST+ is a new tool designed to identify macromolecules that have similar 3-dimensional structures, with an emphasis on finding similar macromolecular complexes. The similarities are calculated using purely geometric criteria, without regard to sequence similarity, and therefore can identify distant homologs. VAST+ is built upon the original Vector Alignment Search Tool (VAST), and expands the capabilities of that program by taking into account the biological unit ("biounit") of each structure, not just individual protein molecules or their substructures. A recent publication provides details and the VAST+ help document includes a comparison of original VAST and VAST+, as well as examples of how can VAST+ be used to learn more about proteins. (Please note: in order to view the 3D superpositions of similar biological units, you must install the most recent version of the NCBI molecular viewing software, Cn3D 4.3.1.)

VAST+ search results for 1B26 Glutamate Dehydrogenase (Thermotoga maritima)  
(as of 02 Dec 2013, with detailed view of match to 1GTM)
Detailed comparison of a query structure and a VAST+ similar structure, listing names of aligned molecules and alignment statistics, for the alignment of 1B26 (Glutamate Dehydrogenase from Thermotoga maritima) and 1GTM (Glutamate Dehydrogenase from Pyrococcus furiosus). Click on the image to open a live web page with VAST+ results for 1B26.

Open a live web page with VAST+ results for 1B26

[06 DEC 2013]  Cn3D 4.3.1 is now available.  A new version of NCBI's macromolecular structure viewing program, Cn3D 4.3.1, is now available (download). New features include the ability to view superpositions of 3D structures that have similar biological units, as identified by the newly released VAST+, an enhanced version of the Vector Alignment Search Tool. In addition, Cn3D 4.3.1 now uses the MIME type: application/vnd.ncbi.cn3d. Up to version 4.3, Cn3D used the MIME type: chemical/ncbi-asn1-binary.

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Conserved Domains and Protein Classificationback to top

[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.

[28 MAY 2015]  A new version of the Conserved Domain Database (CDD) has been released. Version 3.14 contains 560 new or updated NCBI-curated domains, including models specifically built to annotate structural motifs (accession prefix "sd"), and contains corrections to some short names for TIGRFAM records as well as updated names and classifications for many models derived from COGs. A fine-grained classification of the Myosin motor domains has been added. 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.

[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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PubChemback to top

[17 AUG 2015]  The Laboratory Chemical Safety Summary (LCSS) view is now available in PubChem. An LCSS is a summary of a hazard and safety information for a chemical, including flammability, toxicity, exposure limits and symptoms, first aid, handling, clean up, and so on. To learn more about PubChem LCSS please read the PubChem Blog.

[23 JUN 2015]  The PubChemRDF 1.5β is now available. The new version is faster, supports Linked Data in new formats, features improved search and query functions, and contains new links. To learn more about this, visit the PubChem Blog.

[09 APR 2015]  A new PubChem Substance Record page is now available. It replaces the previous PubChem Substance Summary page. Similar to the recent update to the PubChem Compound Summary page, this page was given a substantial makeover. Detailed information on the new PubChem Substance Record page is provided in the PubChem Blog.

[20 OCT 2014]  A revamped PubChem Compound Summary page is now available. Technology has advanced considerably since the last major update in 2011, so this page was given a substantial makeover. Detailed information on the new PubChem Compound Summary page is provided in the PubChem Blog.

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BioSystemsback 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 24 August 2015