What's New in this Release (December 7, 2010)

Table of Contents:
  Ligand Features
  Tabular Reports
  Data Drill-down
  General Site Improvements

Personal Structure Annotations With MyPDB

MyPDB now allows you to save personal annotations and notes on the structure summary tab of any entry. You can also "tag" an entry to add it to a "favorites list".A summary page (click here) lets you easily access all of these tagged structures and annotations. All information stored using this new feature will be saved in your MyPDB account.


Transporter Classification Database Browser

The Transporter Classification Database (www.tcdb.org) organizes membrane transport proteins using the Transporter Classification (TC) system. It is similar to the Enzyme Commission (EC) system, but incorporates both functional and phylogenetic information. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. Transport systems are classified on the basis of five criteria, and each of these criteria corresponds to one of the five numbers or letters within the TC number for a particular type of transporter.

The RCSB PDB database can now be browsed using this TC system. Select the Transporter Classification tab from the Browse Database interface to browse TC superfamilies, view the number of associated PDB structures, and explore for the individual structures.

Advanced Search can be used to combine searches for transporter classifications with queries for other specific types of data. Select the Transporter Classification Browser option from the Biology section of the Advanced Search pull-down menu.


Structural Biology Knowledgebase Widget

The Structural Biology Knowledgebase (SBKB) is a free, comprehensive resource that integrates the results of structural biology and genomics efforts with other publicly available biological information to facilitate further research.  A new widget on every RCSB PDB Structure Summary page links the related information at the SBKB. It asynchronously loads data about available models, protein targets, related biological annotations, related clones and PepcDB related protocols with links to SBKB reports page.

The SBKB is part of the Protein Structure Initiative:Biology Network and funded by NIGMS.

Ligand Features

Ligand Download Page

The Ligand Download page is available from the left-hand menu of the web page, from the "Display/Download" drop-down menu of the "Ligand Hits" tab" of a query results page, and from the Ligand Summary page. It can be used to download Structure Data files (SDF) for one or more ligands.

The Structure Data File (SD-Format V2000) is one of the most popular chemical structure file formats (Dalby et al., J. Chem. Inf. Comput. Sci. 1992, 32: 244-255). A single SDF file can comprise multiple small molecules and associated data.

You may download SDF data with either experimental coordinates from PDB files (ligand instances), or idealized (software generated) coordinates from the Chemical Component Dictionary.

The page provides various "Download","Filtering" and "Instance type" options that can simplify the task of extracting useful experimental coordinate data for drugs and ligands in the PDB.


Ligand Images on Structure Summary Page

To improve the usability of the ligand data the Ligand Chemical Component, External Ligand Annotations and Modified Residues boxes now include an image of each ligand that is present. You can hover over the image to see a larger preview, or if you click on it, it opens the large version of the image in a shadowbox and provides you with a link to download it.


Integration of Binding Affinity Data From BindingMOAD Database

Binding affinity data from BindingMOAD (http://www.bindingmoad.org/) have been integrated with the RCSB PDB website, after the integration with BindingDB in the last release. A new orange Ligand External Annotations widget in the Structure Summary page lists available binding affinity data from both BindingDB and BindingMOAD. The data are linked to BindingDB and BindingMOAD details pages, respectively.

The BindingMOAD data can also be queried through Advanced Search to find PDB entries of protein-ligand complexes with associated binding affinity data. IC50, EC50, Ki, and Kd must be specified in nM, thermodynamic data ΔG, ΔH, -TΔS in kJ/mol, and Ka in M-1.

Tabular Reports

Binding Affinity

A Binding Affinity category has been added to the customizable table to allow users to include associated binding affinity data for PDB entries.


Structural Genomics Centers

A predefined report for Structure Genomics Centers is accessible from the Generate Reports drop-down list. Select Structure Genomics Centers under Summary Report on the result page. A new category that includes the Structure Genomics Center details has been added to custom reports as well.

Data Drill-down

Drill-down by Enzyme Classification Number

The pie charts available from the top of each results page now include summary statistics and drill-down links based on the Enzyme Classification system. The drill-downs are ideal for the EC system due to its hierarchical nature and allow users to restrict their results from any type of search (text, sequence etc) according to enzyme classes of interest in just a few mouse clicks. The summary charts provide a quick look at types of structures in the query results, and can be used to filter outliers or focus in on interesting results.


Drill-down by SCOP Domain

The SCOP drill-down interface is another summary pie chart option. It can give a quick look at the domains that are included in a result set, and can be used to restrict them in entries that contain SCOP domains of interest.


Two-Dimensional Macromolecule-Ligand Interaction Diagrams

The display of 2D macromolecule-ligand interaction diagrams is a new feature on the Structure Summary page. The diagrams, generated by PoseView, depict the structure diagram of the ligand and interacting residues. A thumbnail image is displayed in the Ligand Chemical Component widget under the "Interactions" header. By clicking on the thumbnail image, a full-size image will be displayed that may also be saved.

In a PoseView image, black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions.

Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB.

PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.

For details on the PoseView layout algorithms see also:

K. Stierand, M. Rarey (2007), From Modeling to Medicinal Chemistry: Automatic Generation of Two-Dimensional Complex Diagrams, ChemMedChem, 2, 853-860, DOI: 10.1002/cmdc.200700010

Stierand, K., Maaß, P., Rarey, M. (2006) Molecular Complexes at a Glance: Automated Generation of two-dimensional Complex Diagrams. Bioinformatics, 22, 1710-1716, DOI: 10.1093/bioinformatics/btl150


High-resolution Image Generation

Simple Viewer, Protein Workshop, and Ligand Explorer have a new option for saving high-resolution images in JPEG, PNG, and TIFF formats. The width and height of an image can be specified in pixels or in physical dimensions of inches and millimeters. This feature is useful for journal publications, where images of a particular size and resolution specified in Dots Per Inch (DPI) are required, and for high-resolution prints.

The Save Image dialog box is available from the File menu for the viewers listed above. The image to the left shows an example of the Save Image dialog box with custom settings for an image of size 11 x 8.5 inches with a print resolution of 300 DPI to be saved in the JPEG format. The image file type can be selected from the "Files of type" menu.


Jmol Page Option Panel

We have now reorganized the Jmol page to simplify the menu options, which are now available from pull-down menus instead of radio buttons.


Improved alignment display

We have enhanced the display of sequence alignment results to color-code the alignment according to the degree of similarity. We are now also using a color palette which is more legible for color blind individuals.

Residues are colored as follows:
Black - identical residues
Pink - similar residues
Brown - sequence mismatch
Blue - insertion/deletion

General Site Improvements

Support for Chemical Shifts Files

As previously announced, effective December 6, 2010, deposition of chemical shift data will be mandatory when submitting NMR entries to the PDB.

Following the public release of structures deposited under this new policy, the associated chemical shifts files will be available for download from the Structure Summary page. In addition, the PDB Current Holdings Breakdown will list the number of structures in the PDB that have a chemical shifts data file.


Redesigned Help System

We have carefully replaced our help system with a new intuitive system that presents help items in a shadow box with the option to "pop out" the help page into a separate window.


Orange Color for External Resources

We have changed the way we display data that has been loaded from external resources by highlighting them with a new color. All external annotations are now contained in orange colored boxes instead of our regular blue ones to hightlight the difference between our primary and externally gathered data.