What's New in this Release (November 29, 2011)

Table of Contents:
  Ligand Related Features

Molecular Surfaces in Protein Workshop

Creating molecular surfaces

Protein Workshop now supports molecular surfaces to aid in the display of quaternary structure, protein-protein interactions, and binding sites. Protein Workshop can be launched on the right hand panel on every structure summary page. Surfaces are created for all macromolecule chains in a PDB entry using the algorithm from D. Xu, Y. Zhang (2009) Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform. PLoS ONE 4(12): e8140

To turn on surfaces, move the surface transparency slider all the way to the right to display an opaque surface. Move the slider to the left to increase the transparency. Surfaces can be turned off by moving the slider to the off position.

Transparent surfaces look best on a white or light colored background. The background color can be changed on the Shortcuts tab.

Coloring surfaces

Surfaces can be colored by four properties:

Chain: each macromolecule chain is rendered in a different color or shade of color

Entity: unique macromolecule chains with identical sequence are colored the same

Single Color: all chains are colored by the same color

Hydrophobicity: residues are color coded according to hydrophobicity

Coloring by chain and entity

Chains and entities are colored by color schemes, which are carefully chosen combinations of colors or shades of color.

There are three types of color schemes available: sequential, diverging, and qualitatitive. The default color palette (5 colors) will be adjusted by the number of chains or number of entities to render the surface. In case there is only a single chain or entity, try the Single color option instead. All colors of the sequential color scheme are colorblind safe, however, not all colors schemes from the diverging and qualitative colors are colorblind safe. A description for each color scheme is available as a mouse-over. These color schemes have been adopted from ColorBrewer developed by C. Brewer, The Pennsylvania State University.

The color scheme selected in the above example will give the following result:

Toggling transparency and changing color of a selected surface

The visibility and color surfaces for selected chains can be adjusted using the Visibility and Colors tools from the toolbar after surfaces have been generated for all chains in a PDB entry.

To change the transparency of a specific surface:
  • 1. Choose Visibility
  • 2. Choose Surfaces
  • 3. Choose a chain.

To change the color of a specific surface:

  • 1 select the Color tool
  • 2. Choose Surfaces
  • 3. Choose a chain.

Surfaces for large biological assemblies

The surface generation code is able to handle very large assemblies, such as virus capids.

Tips for manipulating surfaces

When displaying a large assembly such as a virus capsid, turn visibility of the ribbons off. This will significantly decrease memory requirements and will increase the responsiveness of the application. Parts of ribbons occasionally protrude through the molecular surface. Again, turning off ribbons will solve this problem.


Improved Jmol Page

In this release, we simplified the layout for Jmol, our most popular 3D viewer. The "Display options" has been further streamlined for easy use. Advanced users familiar with the Jmol-scripting language can send script commands from the input-box. The bottom panel offers several options. The default view is the annotation tab; users can click on various annotations to their location on the 3D structure. The history tab displays the Jmol-script command history, which can be useful for learning how to work with Jmol. The console tab shows various log messages from Jmol, and the Help tab provides links for more documentation.

Ligand Related Features

Ligand Images

New options for the Jmol display, including new large ligand chemical diagrams, make viewing and understanding large ligands from the Ligand summary pages much easier. These diagrams can be displayed either with or without atom labels. The Jmol widget (found on the Ligand Summary page for any ligand, for example 2NC) can now be re-sized to improve 3-D viewing. New "Toggle" checkboxes for "Hydrogens" and "Labels" are also included.

New links below the ligand image, will display a "Large image" chemical diagram of the ligand that includes atom labels corresponding to the atom names found in HETATM records in PDB files.


Subcomponents and Leaving Atoms

The Ligand summary pages now provide information about molecules that have been annotated as having sub-components. For example the ligand 0ZX is composed of the sub-components BOC ALA VAL and 0AY that are connected with peptide-like or other bonds. Similarly the pages provide notations for atoms that are cleaved when the chemical component is linked to another molecule. For example, in the ligand 0ZX, OXT is noted as a "Leaving atom".


Links to DrugBank

The Ligand summary page also provides links to DrugBank, a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. The link for Ligand 1UN for example, refers to the DrugBank entry "DB00220 - Nelfinavir" which provides detailed information about this drug.


Binding Affinity from PDBBind

Binding affinity data from PDBbind (http://www.pdbbind-cn.org) have been integrated with the RCSB PDB website after the integration with BindingDB and BindingMOAD in the previous releases. BindingDB, BindingMOAD and PDBbind are the three binding affinity databases.

The orange Ligand External Annotations widget in the Structure Summary page lists available binding affinity data from the three resources. The data are linked to BindingDB, BindingMOAD, and PDBbind details pages, respectively. Users can easily access any of them with one mouse click.

The data sets in the three resources have some overlaps but more differences. Some structures may only have binding data available in one of the databases.


Autocomplete Improvements

The autocomplete suggestions of the top bar search are faster and more prominent. Users are given a chance to view suggestions before they perform a search and the suggestions pop-up widget is more responsive.


Webservices for Pre-released Sequences

Webservices for pre-released sequence is an extension of searching for unreleased structures. User can get the pre-released sequence in FASTA format by calling this webservices.

It will return all the unrelased sequences if no parameters are sent in, or will return a subset of PDB IDs sequences. The value for parameter entity type is DNA, RNA, and Polypeptide. It also take the parameter deposition date.

For example: /pdb/rest/getStatusSequence?entityType=RNA&depositionDateMin=2011-07-01&depositionDateMax=2011-07-31 will fetch the pre-released nucleic acid sequences deposited between 07/01/2011 and 07/31/2011.


FAQ Pages

The Website FAQ and PDBMobile FAQ have been revamped for easier navigation and greater readibility. Information related to system requirements and supported browsers have been updated as well.