Tuesday, March 19, 2013

Trendspotting in the Protein Data Bank

Our most recent article has become publicly available. It describes some of the trends that we can observe in the Protein Data Bank:

Trendspotting in the Protein Data Bank. FEBS Letters, (0). Berman, H. M., Coimbatore Narayanan, B., Costanzo, L. D., Dutta, S., Ghosh, S., Hudson, B. P., Lawson, C. L., et al. (n.d.). doi:http://dx.doi.org/10.1016/j.febslet.2012.12.029


Friday, March 8, 2013

Spring 2013 release of RCSB PDB

This week we released the spring 2013 release of the RCSB PDB's website. This release was a lot of work and we added a ton of new features and improvements. Here my wrap-up of some of our highlights. For a full listing see the What's New page for more features and examples.

Protein Symmetry and Stoichiometry

The calculation of protein symmetry and stoichiometry is one of the major features of this release. The goal is to better describe biological assemblies of proteins according to some of their characteristics.

Symmetry refers to the point group symmetry of a protein complex. Protein complexes with quaternary structure can have rotational symmetry belonging to the point groups: cyclic (Cn), dihedral (Dn), tetrahedral (T), octahedral (O), or icosahedral (I). 

The stoichiometry of a protein complex represents the composition of its subunits. For example, the biological assembly of hemoglobin has two alpha and two beta subunits, represented by the formula A2B2.

Here a few examples:

The Crystal structure of the Clostridium perfringens NetB toxin in the membrane inserted form
has a cyclic symmetry of C7 and is formed by a homo-7-mer (A7)

The Crystal structure of phosphoserine phosphatase from T. onnurineus has Dihedral - D4 symmetry and is formed by a homo-8-mer (A8)
The Plasmodium falciparum malaria aminopeptidase has Tetrahedral symmetry and is a homomer composed of 12 chains.

Ferritin has Octahedral symmetry and is a Homo 24-mer

The Foot-and Mouth Disease Virus has Icosahedral symmetry and is formed by a Hetero-240 mer with the a A60B60C60D60 stoichiometry.

Tip: Enable the Axes and Polyhedron options on the Jmol page to get a better understanding of the composition of the protein.

Biologically Interesting Molecules

Various biologically interesting molecules, such as peptide-like antibiotic and inhibitor molecules are being annotated by the PDB. The latest RCSB PDB website provides better access to these data. These molecules are now search-able in the top-bar search, and we provide better reports and visualisation.

Access to Drug Targets in the PDB 

For this release we integrated drug and drug target data from DrugBank (www.drugbank.ca). For example: look up Ibuprofen .

We also provide access to the Anatomical Therapeutic Chemical (ATC) Classification System, which is used for drug classification.

Better site navigation

We have re-designed our page header and given it a cleaner and simpler feel.

Uniprot Gene Names

We added a new search function for Gene names. Proteins that can be linked to PDB via Uniprot can now be identified by their associated gene annotations.

SCOP track in Protein Feature View

 The Protein Feature View now has a new track - domain annotations from SCOP. Example: Obelin

This was just a quick summary of some of the new features. For a complete list, take a look at the What's new page.