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

[__ MAR 2014]  A new version of the Conserved Domain Database (CDD) has been released. Version 3.12 contains 1526 new or updated NCBI-curated domains. You can access CDD from http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml and find updated content on the CDD FTP site at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd. Database statistics, showing the number of domain models from each source database, are provided on the CDD News page.

[12 FEB 2014]  The display style for drawing domain models in CD-Search, Batch CD-Search, and CDART has been revised. The display style is now uniform among those tools, with a given domain model rendered in the same shape and color by all three tools. Additionally, a new display option, "Standard Results," is available in CD-Search and Batch CD-Search, and shows the top-scoring domain model from each source database. The Batch CD-Search graphical display of search results also offers a new "compact mode," which displays the domain architecture of each query sequence on a single line. This display type is particularly useful if you select two or more query sequences from the list and want to compare their domain architectures. All three tools (CD-Search, Batch CD-Search, and CDART) employ the latest version of RPS-BLAST, which, as of version 2.2.28, uses composition-based scoring and abolishes the need to mask out compositionally biased regions in query sequences. Live and pre-computed searches generated by the CD-Search web tool now use these settings, and as a result the domain annotations have changed for a number of protein sequences in Entrez.

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PubChemback to top

[30 JAN 2014]  PubChem RDF is released! It allows PubChem data to be used with semantic web technologies and encodes PubChem information using the Resource Description Framework (RDF). PubChemRDF data can be accessed through a REST interface or bulk downloaded from the PubChem FTP site. One benefit of RDF formatted data is the ability to use schema-less databases (such as a triplestore or a graph database) to import, query, and analyze PubChem data locally. Read the PubChem Blog (http://1.usa.gov/1db9Y4T) to learn more.

[21 NOV 2013]  PubChem Upload 1.0f is released! Adding your information to PubChem is now easier than ever. The new PubChem Upload system offers streamlined procedures for data submissions and includes an extensive set of wizards, inline help tips, and templates to assist users. Visit the PubChem Blog to read more about it.

[03 SEP 2013]  The PubChem Social Media campaign is now launched! Follow us on Twitter, Facebook, and Google+ to keep up with the latest PubChem resources and features. Share PubChem pages with your friends and colleagues. Visit the new PubChem blog to read more about it.

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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 __ September 2014