3D Macromolecular Structures

[09 MAY 2011]  New structure summary pages featuring biological units and interactions.  MMDB structure summary pages have been revised to display salient features of each structure, including its biological unit(s) and an interaction schematic depicting the interactions among the structure's molecular components, as in the human hemoglobin example below. The procedures to identify a structure's biological unit(s) and thresholds used to display interactions are described in the help document.

[25 MAY 2011]  Cn3D 4.3 now available.  A new version of NCBI's macromolecular structure viewing program, Cn3D 4.3, is now available. New features include the ability to view biological unit(s), including those containing molecules generated by applying transformations from crystallographic symmetry, side by side stereo views, and more (download).

ASYMMETRIC UNIT (RAW DATA) IN THREE DIFFERENT STRUCTURE RECORDS FOR HUMAN HEMOGLOBIN: BIOLOGICAL UNIT IS SIMILAR IN ALL PDB ID: 2DN2 MMDB ID: 39206 PDB ID: 1LFT MMDB ID: 20898 PDB ID: 1LFL MMDB ID: 20896 MMDB summary page displays the biological unit by default: Complete tetramer of human hemoglobin Half of the tetramer, which can be used to reconstruct the complete tetramer by applying transformations derived from crystallographic symmetry Two copies of the tetramer   and an interactions schematic:

Conserved Domains and Protein Classification

[28 MAR 2012]  Conserved Domain searches are now being launched for all nucleotide queries shorter than 10,000 base pairs submitted to blastx, the BLAST program that translates a nucleotide query sequence in six reading frames and compares each translation against the protein data set. The blastx search results page includes a concise display of the conserved domains found on the translated reading frames, and that graphic links to the corresponding interactive view in the CD-Search tool.

[04 NOV 2011]  The CD-Search tool now accepts nucleotide sequences as queries. It translates them in all six reading frames and searches each protein product against the RPS-BLAST databases. CD-Search will combine the results for all the proteins into a single page, but will only display the translated reading frames that picked up a match in CDD. The help document provides additional details.

PubChem

[24 APR 2012]  PubChem PUG REST -- a RESTful web interface to PubChem data and services. Documentation and examples are available at http://pubchem.ncbi.nlm.nih.gov/pug_rest/. This service is considered to be in a beta state right now, meaning it is under active development and some changes may occur but the interface should be mostly stable. The purpose of this beta release is to make some basic functionality available now, and to invite feedback from the PubChem user community. Please try it out and tell us what you think; contact pubchem-help@ncbi.nlm.nih.gov with questions, problems, or suggestions for new features.
[21 FEB 2012]  Structures from Therapeutic Target Database (TTD) are now available in PubChem.

BioSystems

[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.