Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank

Summer 2009
Number 42

 
NEWSLETTER
  Contents  
Home | Newsletter Archive | PDF Version
Message from the RCSB PDB
Data Deposition
5 Easy Steps for Structure Deposition
Improve the Quality of Your Depositions with SFCHECK
How does an HPUB structure get released?
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
Literature View: Looking at Structures in PubMedCentral
Customizable Structure Summary Pages
MyPDB: Keep up-to-date with new structures... automatically!
Ligand Expo: Searching and Browsing Features
Outreach and Education
Recent and Upcoming Meetings and Presentations
Congratulations to National Tournament Champions
wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe
Looking at Structures: A Resource for Learning About PDB Data
Education Corner
Community Outreach
PDB Community Focus
Gregory Warren, OpenEye Scientific Software, Inc.
RCSB PDB PARTNERS, MANAGEMENT, AND STATEMENT OF SUPPORT
 
       

Message from the RCSB PDB
Overview of Online Enhancements

This spring, the RCSB PDB added new features and functionality that modernized the look and feel of www.pdb.org. A full list of features included in this release is available online, with many of these new items highlighted below and in the newsletter.

Quick searches by PDB ID or keyword, author name, structural genomics center, and chemical component name and ID are available from a new pull-down menu offered on every page.

Icons are used to indicate links to help pages ( ), molecular viewers ( ), database searches ( ), and external sites ( ). Holding your mouse cursor over a search field or active link will display more information about these options.

The Ligand Explorer viewer option on Structure Summary pages can be used to dynamically view hydrogen bonds, hydrophobic contacts, bridged H-bonds, metal interactions, and neighbor residue interactions and thresholds.

Customizable Structure Summary pages let users highlight particular types of information. Boxes ("widgets") can be clicked and dragged, and their content hidden or shown. New layouts are automatically stored for future visits. An online video screencast demonstrates how to customize the layout of this page.

Other new features include a Literature Tab View that incorporates PubMed- Central abstracts and images, and a Sequence Similarity Tab View that provides an overview of the sequence clusters for each protein chain in a PDB structure.

 
Snapshot: July 1, 2009
58588 released atomic coordinate entries
Molecule Type
54141
proteins, peptides,
and viruses
2033
nucleic acids
2381
protein/nucleic acid
complexes
33
other
Experimental Technique
50284 X-ray
7914
NMR
243
electron microscopy
17
hybrid
130
other
 
39459
structure factor files
5200
NMR restraint files

 

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