Systematic Detection of Internal Symmetry in Proteins Using CE-Symm

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.

Read more over at JMB.

Several protein domains with internal symmetry that CE-Symm detects. Coloring is by symmetry unit.

BioJava 3.0.8 released

 BioJava 3.0.8 was released on March 25th 2014 and is available from

http://biojava.org/wiki/BioJava:Download as well as from the

BioJava maven repository at http://www.biojava.org/download/maven/

This release would not have been possible without contributions from

13 developers, thanks to all for their support!

BioJava 3.0.8 includes a lot of new features as well as numerous bug fixes and improvements.

New Features:

•  new Genbank writer
•  new parser for Karyotype file from UCSC
•  new parser for Gene locations from UCSC 
•  new parser for Gene names file from genenames.org
•  new module for Cox regression code for survival analysis
•  new calculation of accessible surface area (ASA)
•  new module for parsing .OBO files (ontologies)
•  improved representation of SCOP and Berkeley-SCOP classifications

 

For a detailed comparison see here:

https://github.com/biojava/biojava/compare/biojava-3.0.7...biojava-3.0.8

For the next release we are planning some refactoring and removal of code that has been deprecated for a long time. As such the next release will be named 3.1.0.

About BioJava:

BioJava is a mature open-source project that provides a framework for

processing of biological data. BioJava contains powerful analysis and

statistical routines, tools for parsing common file formats, and

packages for manipulating sequences and 3D structures. It enables

rapid bioinformatics application development in the Java programming

language.

Happy BioJava-ing,

Andreas

RCSB PDB September 2013 release

This week we released the latest RCSB PDB web site update. 

 The main new features are:

- 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!

Workshop on Sustainable Software for Science: Practice and Experiences

Interested in sustainability of scientific software?

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

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

http://www.sciencedirect.com/science/article/pii/S0014579313000240

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.

Example: All structures that contain Vancomycin

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.

Protein Feature View goes open source

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).