Friday, April 25, 2014

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.

Tuesday, March 25, 2014

BioJava 3.0.8 released

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

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
  •  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:

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

Happy BioJava-ing,