The April 28, 2015 release offers the following features:
Support forLarge Structures
Protein FeatureView Enhancements
Mapping Genomic Position toSequence and Structure
PV displays symmetric structures aligned along the symmetry axes. In addition, two of PV's unique features include "out of the browser" views:
Large structures (containing > 62 chains and/or 99999 ATOM lines) represented as single files have been fully integrated into the main PDB FTP archive in both PDBx/mmCIF and PDBML formats since December 10, 2014.
A new search option has been added to Advanced Search under the category Structure Annotation to find "Large Structures", i.e., structures that do not fit into the legacy PDB file format. This search can be used to find all structures that have PDB format files, or those that do not.
Previously, large structures were represented in multiple "SPLIT" entries. These "SPLIT" entries have now been superseded by a single entry. This information is listed on the Structure Summary page of these entries.
In addition, Structure Summary pages of large structures contain a download link to a compressed archive file (tar.gz), which contains a collection of minimal/best effort files in PDB format to support legacy application. Please see this Usage Note for more details. These tar files can also be downloaded in batch, using the Download Tool. Users and developers are urged to adapt to using the PDBx/mmCIF files, rather than the legacy PDB files, to take full advantage of the archive.
The Protein Feature View has a new option to select Protein Feature Views from related organisms with the same gene name.
The Action button contains an option to map sequence motifs in the Protein Feature View as shown below.
Mutations in a gene can have profound effects on the function of a protein. A new analysis tool highlights the location of a gene location (i.e., the site of a SNP).
A TGT-to-GGT transversion in codon 64 of the BRCA1 gene leads to substitution of glycine for cysteine. This SNP is located on chromosome 17 at genomic coordinate: 43,106,478. The new mapping tool can be used to locate this position on UniProt sequence and 3D structure
The Download Tool can be used to download multiple structure, experimental data (structure factors, NMR restraints), sequence, and ligand files in various file formats in uncompressed and compressed (gzipped) form. Large structures without PDB formatted files can be downloaded as compressed archive files (tar.gz), containing collections of minimal/best effort files in PDB format to support legacy applications.
This tool replaces our earlier Download Applet and requires an up-to-date Java installation (Browser Compatability Check).
The Download Tool is launched as a stand-alone application from the RCSB PDB website using the Java Web Start protocol.
The download page also offers links to download FASTA sequence files and SDF ligand files for the entire archive.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.