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What's New
 
   3D Macromolecular Structures   Conserved Domains   PubChem   BioSystems 
 

3D Macromolecular 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 Tumor Suppressor P53 Complexed with DNA (1TUP) in its MMDB structure summary page, or open it directly in the basic version or advanced (full feature) version of iCn3D.
The source code is available from GitHub (https://github.com/ncbi/icn3d) 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 Classificationback 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 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.

[30 JUN 2015]  An updated version of the "rpsbproc" command line utility for RPS-BLAST is now available from the CDD FTP site: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/. 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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PubChemback to top

[10 MAR 2016]  On March 13-17, 2016, the 251st American Chemical Society National Meeting will be held in San Diego, CA, the theme of which is "Computers in Chemistry". 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 the PubChem Blog.

[19 JAN 2016]  A new article about the PubChem Compound and Substance databases can be found in the 2016 Nucleic Acids Research Database issue. It provides an overview of the two databases, including data organization, contents, interfaces, programmatic access and other relevant tools and services. To learn about this and other recent PubChem publications, read 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 27 June 2016