RCSB PDB Newsletter | Fall 2013 ⋅ Number 59

Data Query, Reporting, and Access

New and enhanced features have been added to the RCSB PDB, including:

Drug and Drug Target Mapping

Two new tables provide access to drug and drug target information from DrugBank mapped to PDB entries. These tables, accessed from the Tools menu, can be searched by generic or brand drug name, filtered, and sorted:

  • The Drugs Bound to Primary Targets Table lists drugs bound to primary target(s), or a homolog of primary target(s), i.e., co-crystal structures of drugs.
  • The Primary Drug Targets Table lists primary drug targets in the PDB, regardless if the drug molecule is part of the PDB entry (e.g., apo forms of drug targets, drug target with different bound ligands). Biotherapeutics, such as complexes with monoclonal antibodies, are included.
Protein Symmetry

Options to explore local and helical symmetry have been added to our protein symmetry resources, which include data distribution summaries (on the home page and for search results), Advanced Search, and the Jmol viewer.

The new Protein Symmetry Browser can also be used to browse for structures.

New Jmol/3D View page

The layout of options for viewing a structure in 3D has been improved to provide quick access. Select from views that highlight Secondary Structure, Subunits, or Symmetry, or use the Custom View to utilize different features. All views can be saved as an image file.

The What's New page offers more details on these and other new features.

Sequence Identity Cutoff option in Advanced Search.

Improved Searching with New Sequence Identity Cutoff

A sequence identity cutoff value option has been added to Advanced Search for "Sequence (BLAST/FASTA/PSI-BLAST)". To use this feature, enter a sequence by typing a PDB ID in the Structure ID text box and selecting a Chain ID from the pull-down menu or by pasting a sequence into the Sequence text box.

Using the Sequence Identity Cutoff (a percentage value between 0 and 100) option, the results returned will have at least the specified sequence identity to the target sequence. For example, entering 100% returns entries with exactly match the same sequence. As many structures have low E-values but only a few have high sequence identity with the target sequence, fewer results will be returned when using this feature.

The % sequence identity can be seen by displaying the sequence alignment on the query results page. All results returned will have sequence identity greater than or equal to the cutoff used.

This Sequence Identity Cutoff differs from the 'retrieve representatives' option found at the bottom of the Advanced Search screen and on the Query Results pages. The option to "retrieve only representatives at XX% sequence identity utilizes RCSB PDB's use of BLAST clustering to remove redundant sequences, and returns one representative per cluster.

Ligand Summary Reports include information about chemical components associated with the entries in a results set, such as formula, molecular weight, name, SMILES string, which PDB entries are related to the ligand, and whether the chemical component is included as a free ligand or as part of the polymer chain.

For each ligand, a sub-table can be selected to list all related PDB entries that contain the ligand, the entries that contain the ligand as a free ligand, and entries that contain the ligand as part of a larger, polymeric ligand.

To display this sub-table, select the triangle shown next to the Ligand ID. The display is limited to 15 PDB IDs in each column. For ligands associated with more than 15 PDB entries, the ... [more] link will launch a query for that set of structures.

All tabular report features are also available, including sorting, filtering, export to other report formats, and column customization.

To generate a report, select the Ligand Hits tab for any set of query results.

The Generate Reports options available for Ligand Hits includes a collage of ligand images, or the Ligand Summary Report.

Click on the triangle to reveal the sub-table of PDB IDs.

Beta #11 of the Android version of RCSB PDB Mobile app is available for download. This will likely be the final beta release before the app becomes available in the Google Play store.

Requirements:

  • It will only supported on Android version 4.0 or above, though it may be installed on earlier Android versions above 2.3.3
  • 35mb storage is required for installation, with an additional 60mb of storage is required to store the app's internal index
  • This release does not support tablet devices; that support will be implemented in a future update
RCSB PDB Mobile is also available from the Apple App Store.

Gallery view for a search for structures with tetrahedral symmetry. Images can be resized, and entries can be selected or deselected.

Query results can be browsed using detailed, condensed, timeline or gallery views. These views are synchronized; selecting or deselecting a structure in one view will have the same effect in the others.

To view only the images of structures that match a given search, select View>Gallery from the option offered. Moving your mouse over each image in the collage displays the structure title; clicking on the small image shows a larger version. The PDB ID listed links to the corresponding Structure Summary page; the PDB IDs can also be hidden from the gallery.

Protein Feature View for all entries with UniProtKB ID Q13627. This image can be exported as an SVG file.

The new Protein Feature View visually summarizes how a full-length protein sequence from UniProtKB corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder (computed with JRONN) and hydrophobic regions (as computed using a sliding window approach) are also displayed.

For individual entries, the Protein Feature View is available from the Molecular Description Widget on Structure Summary pages. The view illustrates how the ranges of a protein that have been observed in an experiment correspond to the full length UniProtKB sequence, and displays the secondary structure information from the PDB entry. Active sites (from UniProtKB and the PDB entry) are also annotated.

This view can be expanded to map all PDB entries related to a single UniProtKB sequence by selecting the Protein Feature View link shown in this widget. By default, a few representative PDB entries are used to give an overview for which regions of the UniProtKB sequence PDB entries are available.

The PDB to UniProtKB mapping is based on the data provided by the Structure integration with function, taxonomy and sequence (SIFTS) initiative.

The website statistics for the third quarter of 2013 are given below.

Month Unique Visitors Visits Bandwidth
July 2013 263698 655005 1392.55 GB
August 2013 259057 623656 1228.01 GB
September 2013 310025 733943 1505.25 GB