In our latest paper, "Systematic Detection of Internal Symmetry in Proteins Using CE-Symm", we are taking a look at how internal symmetry in proteins is related to protein function. A large number of proteins have symmetry not only in their biological assemblies, but also within their tertiary structures. To investigate the question of how internal symmetry evolved, how symmetry and function are related, and the overall frequency of internal symmetry, we developed a new algorithm that can detect pseudo-symmetry within tertiary structures of proteins. Our results indicate that more domains are pseudo-symmetric than previously estimated. We establish a number of recurring types of symmetry–function relationships and describe several characteristic cases in detail.
- New tools to search for drugs and drug targets
- Improved interface for 3D visualisation using Jmol/JSmol
- An update to the representation of protein symmetry and stoichiometry.
- Improvements when performing sequence searches.
Jesse redesigned our what's new page and made it look really nice, take a look to see all the details!
Interested in sustainability of scientific software?
First Workshop on Sustainable Software for Science: Practice and
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA) http://wssspe.researchcomputing.org.uk/
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
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:
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.
The source code for the Protein Feature View has been released at github. This allows you to incorporate the dynamic SVG graphics visualizing UniProt and PDB relationships into your own web sites. You can either use the public JSON services provided by RCSB PDB to populate the view, or display your own data (after setting up your own services).