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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

[09 JAN 2015]  A new version of the Conserved Domain Database (CDD) has been released. Version 3.13 contains 286 new or updated NCBI-curated domains, including models specifically built to annotate structural motifs (accession prefix "sd"), and now mirrors TIGRFAMs version 15. 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.

[04 DEC 2014]  A new "rpsbproc" command line utility is now available, as an addition to the standalone version of Reverse Position-Specific BLAST (RPS-BLAST).
Standalone RPS-BLAST ("rpsblast") continues to be packaged with the BLAST executables ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/, as it has been since 2000. It lists the conserved domain models that score above a certain threshold (default set to an evalue of 10), sorted by scores, on each of your query protein sequences.
The new "rpsbproc" utility is available from the CDD FTP site: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/. It post-processes the results of local RPS-BLAST searches in order to provide a non-redundant view of the conserved domains found in your protein query sequences, and to provide additional annotation on query sequences, such as domain superfamilies and conserved sites, similar to the annotation provided by the corresponding web services (e.g., the NCBI Batch CD-Search web service at http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi). The README file provides additional details about the new "rpsbproc" utility.


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PubChemback to top

[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.

[16 SEP 2014]  PubChem celebrates 10 years of service to the chemical biology community! With humble beginnings, PubChem was first launched in Sep. 16, 2004. Through this time, PubChem's focus has remained the same: to provide comprehensive information on the biological activities of chemical substances. To read more about this, visit the PubChem Blog (http://pubchemblog.ncbi.nlm.nih.gov/2014/09/16/ten-years-of-service/).

[25 JUL 2014]  Why contribute your data to PubChem? Maximize the impact of your research. Crosslink your data to key scientific databases. Satisfy data sharing requirements by journals and funding agencies. Flexibility on when your data gets released. Ability to share on-hold data with reviewers and collaborators. To learn more about these, visit the PubChem Blog (http://pubchemblog.ncbi.nlm.nih.gov/2014/07/25/why-contribute-your-data-to-pubchem/).


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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 02 March 2015