New Structure Alignment Features at the RCSB PDB Web Site

With the upcoming new release there will be a couple of new protein structure alignment related features:

*) The RCSB PDB web site is providing a structure alignment service. This service can calculate structure alignment on the server side. It also caches all alignments. This means if you come back the next day you can view the same result quickly.

Preview the new alignment service here:
http://betastaging.rcsb.org/pdb/workbench/workbench.do





*) Circular Permutations (CP) in proteins are difficult for alignment algorithms to detect since they depend on the sequence order. These permutations are re-arrangements of the sequence, resulting in different amino acid connectivity, while conserving the overall 3D shape of a protein. Spencer Bliven has extended the Java version of CE and introduced support for the detection of such permutations. This is achieved by working with an internal representation of the proteins that allows to identify alignments across N and C termini. Since this slows down the calculation about three times, the detection of CP is optional.

View an Example of a Cirularly Permutated protein structure alignment

From multi resistant drugs to multi resistant plants

I have always been critical about the increasing monoculture in agriculture. The combination of powerful herbicides and special herbicide resistant crop has on one side increased yield, on the other side reduced the diversity of available crop strains.

Similar to the way some diseases adjust to our drugs and become resistant, it seems multi- herbicide resistant plants are now also becoming a problem:

http://www.nytimes.com/2010/05/04/business/energy-environment/04weed.html

This should come to little surprise for anybody who knows a bit of history of modern agriculture. There are other examples of monoculture and how evolution and adaption of nature in the end puts the harvest at risk. The most prominent example to day is the Banana:

Modern bananas are not as sweet as they used to be in the first half of the 20th century. The then dominant Gros Michael banana essentially was extinct due to monoculture and the emergence of a fungus, killing this plant. This happened before the 1960ies, so not many people can remember this today. I have never eaten a Gros Michael banana myself, so I can only cite other sources that claim that Gros Michael was a better tasting fruit than the Cavendish variety we are eating today. The Cavendish is resistant to the fungus that killed Gros Michael, but reportedly not as sweet and creamy.

Here more about the history of the banana:

http://www.naturalnews.com/023339_banana_bananas_disease.html

To come back to the beginning of this blog, the emergence of multi-resistant plants should alert all farmers. Growing a variety of different strains should become a priority again.

Integration of open access literature into the RCSB Protein Data Bank Using BioLit

In our latest article we describe how we integrate open access articles from PubMedCentral that mention PDB IDs into the RCSB PDB web site. For every PDB entry it is now possible to see how it has been used in the publicly available literature.

http://www.biomedcentral.com/1471-2105/11/220/abstract

On a side note, I am not impressed about the slow pace with which this article got through the review and publication process. It took months to get this out.