RCSB PDB web site update Fall 2012

New Features at the RCSB PDB web site

 This week the  RCSB PDB released the latest major web site update. Here a quick description of some of the new features.

Protein Feature View

One of the main new features is the new Protein Feature View. It allows to compare the full length protein sequence, as defined by UniProt with the regions that have been determined in 3D and are available together with their coordinates from the Protein Data Bank.  Besides the visualization of the PDB and UniProt relationships, the  new view also adds additional annotations for a more comprehensive understanding of the protein. External data such as Pfam domains or regions for which Homology Models are available from the ProteinModelPortal are indicated. There are also some annotations that are being calculated on the fly: Protein disorder regions, as predicted by Peter Troshin's BioJava implementation of RONN are available as a histogram-style track. Finally, regions with increased hydrophobicity can be spotted by looking at the Hydropathy track.

The Protein Feature View is built using SVG graphics and extensively uses the jQuery-SVG library. Using SVG graphics for a prominently  feature on the site (it is on every protein-explorer page) has become possible since the majority of all modern browsers support these types of graphics nowadays. However, there is still a number of users who are stuck with old browser versions.  According to our web site traffic logs, this number is rapidly declining and we estimate that currently less than 15% of our users can't use the new view. These users won't see error messages on the protein-explorer page, thought.  The graphics will simply not be visible and provide a graceful fallback to the way the page used to look before the graphics were introduced.

 

Better Pfam integration

Another new feature of this release is a better integration with Pfam. Pfam family names are now searchable and one can quickly lookup all protein structures related to these families. Since Pfam is used in structural genomics projects to prioritize targets for crystallization, a possible use case is to look up domains of unknown function (DUFs) and whether 3D coordinates have already been determined for them. As already mentioned above, Pfam domains can be viewed as part of the new Protein Feature View. Weekly up-to-date Pfam-PDB mappings are being calculated by submitting newly released PDB entries to the HMMER3 web site. The details of this process are being described in more detail at the Pfam blog site.

Searching and Reporting

Other improvements of this RCSB PDB web site update include search and reporting improvements. RCSB searches have been improved for better supporting poly-proteins and their sub-components (see screenshot above). There is also better support for searching drug names (and more information about drugs on the Ligand Summary page (e.g. Lipitor), coming from DrugBank . Once a search has been performed, there are now four different types of reports available for investigating the results. Besides the "traditional" search results there is now a "condensed" view, which provides a compact summary of results. The "gallery" provides images for the proteins that have been found in the search. A "timeline" gives a historic overview when proteins were released in the PDB

A full description of all the new features is (as always) available on the What's New Page.

BioJava 2012 paper published

Today the latest BioJava paper was published, describing the BioJava version 3 series .

Thanks to all developers for their contributions, it would not have been possible without them!

Abstract:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref

PDF:

http://bioinformatics.oxfordjournals.org/cgi/reprint/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref

Citation:

BioJava: an open-source framework for bioinformatics in 2012

Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius
Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock
Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L.
Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis

Bioinformatics 2012; doi: 10.1093/bioinformatics/bts494

BioJava 3.0.4 released

BioJava 3.0.4 just hit the servers. This is mainly a bug-fix release addressing a few issues with the protein structure and the disorder modules.

One new feature is that SCOP  can now be either accessed from the original SCOP site in the UK or the Berkeley version.

About Pfam and PDB mappings

Today's blog article is not going to get published here but at the Pfam blog site, where Rob Finn and I wrote about the Pfam and PDB mappings:


Does my family of interest have a determined 3D protein structure?

https://xfam.wordpress.com/2012/05/09/pdb-pfam-mapping/

Systematic domain based structure alignments at the RCSB PDB

At the RCSB PDB web site we habe been providing pre-calculated and systematic protein structure alignments already for about two years. Every week we run systematic structure alignments for newly released proteins across a representative subset of the database and try to identify related proteins based on their 3D shape.

This week we have released a major upgrade to those efforts. Our pre-computed alignments are now using domain information to split protein chains into smaller subunits. We introduced this change because many proteins are built of more than just one domain. In that case our previous results were a bit unclear in the sense that results for any of the domains were displayed together and that made the data more difficult to compare and interpret.

The new domain based procedure is using the SCOP domain assignments where available to define how to break up protein chains. If the structures are too new to be annotated by SCOP (like all newly released proteins), then we use a software called ProteinDomainParser to define domains based on geometric criteria. Even if the algorithm sometimes defines a break point that might not be the same what SCOP would define, it is still interesting if you find structural neighbors with such fragments of proteins.

In addition, this release of the RCSB PDB web site also provides a new display of protein chains and how different sources annotate protein domains (see the image above). This domain summary shows SCOP domains, ProteinDomainParser domains and Pfam domains. Here an example for  a Cyclodextrin glycosyl transferase (3BMV) from Thermoanerobacterium thermosulfurigenes. It is composed of four domains, which are identified by all of the three data sources.

java.sun.com down?!

I just realized that java.sun.com is not reachable  and java.net displays this little message:

Thanks to google cache (all the sites containing the original info are unreachable as well) I found a notification in one of the Java User groups:

Notice: Java.net will be offline starting around noon pacific time (7pm UTC) on Friday, April 27, through noon pacific time (7pm UTC) on Monday, April 30 for scheduled maintenance.

A planned downtime of three days. If we would do that at work we would get into serious trouble! We go through all sorts of efforts to ensure 24/7 availability and even if we have major site updates we don't let that impact our availability.

I noticed this because one of my tomcat instances did now want to start up which was caused by a failing XML- dtd validation. 

Luckily this can be easily fixed by removing the dtd validation in the xml file. However I wonder how many tomcat servers world wide will have similar problems to start up until Monday! Such a long downtime of such "standard" URLs is rather unprofessional IMHO.

On Wikipedia's front page

Our article on Circular permutation in proteins has made it on the wikipedia front page!