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   3D Macromolecular Structures   Conserved Domains   PubChem   BioSystems 
 
  3D Macromolecular Structures back to top  

[20 June 2019]  Bioinformatics publication describes features and applications of iCn3D, NCBI's web-based 3D viewer, and provides examples of its use for interactive structural analysis:

  • Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, Phan L, Ward M, Lu S, Marchler GH, Wang Y, Bryant SH, Geer LY, Marchler-Bauer A. iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures. Bioinformatics. 2019 June 20; pii: btz502. doi: 10.1093/bioinformatics/btz502. [Epub ahead of print] [PubMed PMID: 31218344] [Full Text at Oxford Academic]

[01 April 2019]  Multi-character identifiers for sequences with 3D structures from the PDB.  Advances in experimental methods permit the three-dimensional (3D) structure determination of ever larger biomolecular assemblies. To accommodate this, the RCSB Protein Data Bank (PDB) relaxed their constraint that individual biopolymers (proteins and nucleotide sequences) in 3D macromolecular structure records are labeled by a single character. Specifically, a biopolymer identifier may now be up to four characters long.

  • This change has required NCBI to revise how it treats PDB-derived sequence records.
  • The initial and most visible impact will appear in the release of BLASTDBv5 (see BLAST announcement), which will support multi-character identifiers for PDB-derived sequences. But any software, from NCBI or created elsewhere, that assumes a one-character PDB chain identifier will be affected.
  • These changes will also impact the Molecular Modeling Database (MMDB), which is derived from PDB, and the related structure services. More details about how NCBI structure services are affected will be provided on the MMDB News page once multi-character identifiers are fully implemented in MMDB.

[19 March 2019]  iCn3D 2.6.0 is now available on NCBI web servers and from GitHub (https://github.com/ncbi/icn3d). To view the updated web application, see the example structures below, or use iCn3D's "File" menu to retrieve a structure by its ID or to open a structure file on your local computer. The iCn3D Web APIs document describes how to use the iCn3D structure viewer in your own web page. New features in this release include:

  • It is now possible to align a protein sequence to a 3D structure that contains a similar protein sequence. This can be done by opening the "File" menu and selecting "Align > Sequence to Structure." The resulting dialog box enables you to enter (a) the Sequence ID (or FASTA sequence) of the query protein, and (b) the identifier of a structure-based protein that was found by a BLAST search with a query protein against the Protein Databank Proteins (pdb).
  • As an example, open the iCn3D display of NP_001108451 aligned to 1TSR_A. This shows the human tumor protein 63 isoform 3 (NP_001108451) aligned to the 3D structure of protein chain A from the P53 core domain in complex with DNA (1TSR_A).
  • The default color scheme for sequence-structure or structure-structure alignments is color by sequence "Conservation."
  • The Change Log section of the iCn3D Web API help document lists additional enhancements that have been made to iCn3D since its original release.
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  Conserved Domains and Protein Classification back to top  

[03 APR 2019]  A new version of the Conserved Domain Database (CDD) has been released. Version 3.17 contains 3,272 new or updated NCBI-curated domainsand now mirrors Pfam version 31 as well as models from NCBIfams, a collection of protein family hidden Markov models (HMMs) for improving bacterial genome annotation. A fine-grained classification of the major facilitator superfamily has also been added. You can access CDD from https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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 OCT 2016]  The Subfamily Protein Architecture Labeling Engine (SPARCLE) is now available. It is a resource for the functional characterization and labeling of protein sequences that have been grouped by their characteristic domain architecture. To use SPARCLE, you can either: (1) enter a query protein sequence into CD-Search, which will display a "Protein Classification" on the results page if the query protein has a hit to a curated domain architecture in the SPARCLE database, or (2) search the SPARCLE database by keyword to retrieve domain architectures that contain the term(s) of interest in their descriptions. With either approach, the corresponding SPARCLE record(s) will display the name and functional label of the architecture, supporting evidence, and links to other proteins with the same architecture. Additional information and illustrated examples are provided on the "About SPARCLE" page.


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  PubChem back to top  

[26 MAR 2019]  PubChem's homepage has been redesigned to give you easier access to the information you need, where you need it. The mobile-friendly, responsive design works on the device you want to use. And the streamlined, intuitive interface puts the data you need at your fingertips. To learn more about this, please read this post.

[26 MAR 2019]  On March 31-April 4, 2019, the 257th American Chemical Society National Meeting will be held in Orlando, FL. 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, please read this post.

[18 MAR 2019]  PubChem's summary and record pages have been redesigned with a series of updates both behind the scenes and to your own user experience. These changes will make finding the information you're looking for easier and faster. To learn more about this, please read this post.

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  BioSystems back to top  

[15 NOV 2011]  LIPID Metabolites And Pathways Strategy (LIPID MAPS) data are now available in the BioSystems database. LIPID MAPS is a multi-institutional effort to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, the lipid species in mammalian cells, and to quantitate the changes in these species in response to perturbation. Its data can be retrieved from the BioSystems database by doing a search for: lipid maps[sourcename], or by clicking on the LIPID MAPS data statistic in the "database statistics" box on the BioSystems News page. The BioSystems help document provides more details about the source databases.


[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 26 June 2019