New version of RCSB web site released

The RCSB team just released the next major update of the RCSB PDB web site. Here the main features of this release:

• General Site Improvements
• Improved Layout of Query Results Page
• Latest Structures Widget
• Improved Display for Electron Microscopy Entries
• Jmol Page Visualization Features
• Structure Alignment Improvements
• Structure Alignment Service
• Support for Circular Permutations
• Molecule of the Month Improvements
• One-page Layout for Molecule of the Month
• Molecule of the Month Features Linked to Relevant Entries
• Chemical Component (Ligand) Search Improvements
• Chemical Component Results Display
• Chemical Component Search Form
• Chemical Formula Expression Search
• Molecular Weight and InChI Search
• Superstructure Search
• SMARTS Search
• Chemical Name Auto-Complete
• SDF File Download Option for Ligand Results
• Search for Entries with Non-Standard Amino-Acids/Nucleotides
• Tabular Report Improvements
• Inline Filter vs. Advanced Search
• Customize Columns
• Biological Process, Cellular Component, and Molecular Function GO Terms
• CATH, SCOP, and PFAM Domain Assignments with Residue Ranges

biojava-structure now supports Chemical Component Dictionary

I have updated the BioJava structure data model to support the PDB
chemical component dictionary. This has the benefit that now

* Chemically modified amino acids can be detected (and treated as
amino acids, rather than Hetatom groups)
* It is possible to get a component type for each Group, which allows
to identify ligands.

As a consequence the nr. of amino acids in a chain can change compared
to the previous data representation. As such the loading of chem.
comps is set to "false" by default. It can be configure by the
"loadChemCompInfo" flag in the PDB/mmCIF file parsers.

PDB ID 1A4W - Thrombin with Thiazole-containing Inhibitors. Image source: RCSB PDB

An example where this representation makes a difference is PDB ID 1A4W. This structure contains several Ligands and a chemically modified residue. Without the help of the Chemical Component Dictionary it would have been difficult to correctly represent this protein.

You can get the code either from BioJava SVN, or from the (still slightly experimental) Maven repository at http://www.biojava.org/download/maven/ .