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!

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.

BioJava 3.0.5 released

BioJava 3.0.5 has been released and is available from http://www.biojava.org/wiki/BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ .

New Features:

- New parser for CATH classification

- New parser for Stockholm file format

- Significantly improved representation of biological assemblies of protein structures. Now can re-create biological assembly from asymmetric unit

- Several bug fixes

Thanks to Daniel Asarnow for contributing the CATH parser and Amr Al Hossary and Marco Vaz for their contributions to the Stockholm parser.

BioJava 3.0.3 released

BioJava 3.0.3 has been released and is available from
http://www.biojava.org/wiki/BioJava:Download as well as from the
BioJava maven repository at http://www.biojava.org/download/maven/ .


New Features

BioJava 3.0.3 adds several new features

- Significant improvements for the web service module (ncbi blast and
hmmer web services)

- Fastq parser (ported from the biojava 1 series to version 3)

- Support for SIFTS-PDB to UniProt mapping

- Improved support for working with external protein domain definitions

- Protmod module renamed to modfinder

- Numerous improvements all over the place (several hundred commits
since last release)

- We are also working on an update for the legacy biojava 1.8 series.

This release would not have been possible with contributions from
numerous people, thanks to all for their support!

Happy BioJava-ing!

RCSB PDB web site September update

This week the latest update to the RCSB PDB web site went life. One of the major new features in this release is a new search interface. Alex has redesigned the top bar search box:

If you enter a search term, the new auto-suggest box provides suggestions what you might mean and allows to trigger precise searches, which are powered by an efficient new lookup mechanism in the background (written by Dimitris).

If you are not happy with the suggestions that you see (I can hardly imagine that ;-), you can still press enter and do the full text search across the PDB, which has been there already before.

Another major new feature of this release are the improvements to the PDB101, the educational section of the site. Proteins that are described in more detail as part of the Molecule of the Month articles, now have a Discussed Structure page. A particular nice detail that I want to point out is Greg's new 3D molecular viewer that works on iPhones and iPads. These gadgets usually can't display Jmol, our standard 3D viewer, due to the lack of Java support.  To work around this limitation there is now a new HTML5-sprite base animation. If you access a Discussed Structure page with a mobile device this is displayed and can be rotated left-right by "moving" it with your finger. Other improvements on the educational section are that the molecule of the month articles now show up in search results and you can download an article onto your phone. 

I will describe more new features some other time..

New iPhone app at RCSB PDB (beta)

The latest RCSB PDB release features a first version of an iPhone application. It is provided as a HTML5-based application, which means you can install it without going to the Apple Store. Simply point your iPhone Safari-browser to http://www.pdb.org and click "yes" a couple of times. Best to do this while you are on a wireless connection, since the application installs some data for quicker data access.

Gregg, the author of this application also made a screencast with the installation instructions. You can watch it here:

New RCSB PDB Feature: Faceted Browsing

One of the features I find most exciting at the latest RCSB PDB web site release is "faceted browsing". Similar to an online shopping site, which allows to drill down through product categories, it is now possible to drill down through lists of protein structures using categories like Resolution, Organism, Polymer Type, to name just a few of them.

You can easily start browsing by clicking the total number of structures on top of every page. Since this features has become available (Thanks Dimitris!) I have observed myself to use it all the time and I perform much fewer "advanced queries", because this new feature is so easy and quick to use. Let us know if you want to have additional categories.

October release of RCSB PDB website

The latest release of the RCSB PDB website features a number of exiting new features some of which I will present in more detail during follow-up blog postings.


Above a screenshot of the new Category Browser for the Molecule of the Months.

Here a list of all new features:

Molecule of the Month Improvements

• New Category View
• Molecule of the Month Archive

PDBMobile for the iPhone

• Download Application
• Search PDB & Browse Results
• View the Latest News & Molecule of the Month
• MyPDB
• Save Queries
• Personal Structure Annotations

Query Result Browser Improvements

• Data Distribution by Category for Query Results
• Data Distribution by Category for Entire PDB
• Drill-Down by Categories

Chemical Components

• Integration with Binding Affinity Data from BindingDB
• Binding Affinity Data on Structure Summary Page
• Binding Affinity Advanced Search
• New Ligand Summary Page Layout
• Related Entries
• Related Ligands

Tabular Report Improvements

• Ligand Summary Report on Ligand Hits Tab
• New Fields for Customizable Table

Comparison Tool Improvements

• Stand-alone version supports alignment of SCOP domains

General Site Improvements

• Search Improvements
• Top-Bar Search
• PubMed Abstract Search
• Browse Database
• Auto-Complete
• Source Organism Browser with Common Names
• Sequence Search
• PSI-BLAST Search to Find Distantly Related Proteins
• Low Complexity Filter for Sequence Searches
• Sequence and Structure Visualization Improvement
• Improved Domain Display on Sequence Tab
• New Jmol Display Options
• Left Hand Menu
• MyPDB Widget
• Help Widget
• Glossary of Terms
• Sitemap
• Website Performance Improvements