DATA QUERY, REPORTING AND ACCESS

2010 Website Statistics

Month	Unique Visitors	Visits	Bandwidth
January	176,655	422,065	755.87 GB
February	184,306	434,442	783.75GB
March	210,308	510,434	1,189.17 GB
April	203,139	485,879	978.97 GB
May	199,620	473,973	1,058.45 GB
June	174,582	429,274	869.39 GB
July	154,256	477,825	767.18 GB
August	159,350	396,199	783.32 GB
September	201,919	477,825	1,344.88 GB
October	235,083	556,548	1,434.92 GB
November	243,694	586,250	1,560.29 GB
December	202,236	486,887	968.87 GB

Latest Website Release

New and enhanced features were added to www.pdb.org at the beginning of December, including:

• MyPDB storage of annotations. Log in, view a Structure Summary page, and add a note about the entry in the MyPDB Personal Annotations Widget. That text will appear on that Structure Summary page, and on your MyPDB summary page of personal annotations, every time you log in.
• Access to Transporter Classification information. Browse membrane transport proteins in the PDB archive using the Transporter Classification (TC) system from the Transporter Classification Database (www.tcdb.org).
• Access to Structural Biology Knowledgebase data. From an entry's Structure Summary page, users can see the related models, protein targets, biological annotations, clones, and more as provided by the SBKB (sbkb.org).

For complete descriptions, see the New Features Widget on the RCSB PDB home page.



Protein Workshop can be used to export high resolution images of structures. Shown: PDB ID 3pd2

Binding Affinity Data Integration
Binding affinity data from BindingDB (www.bindingdb.org) and from BindingMOAD (www.bindingmoad.org) have been integrated with the RCSB PDB website.

When available, binding constants and thermodynamic data will appear in the External Ligand Annotations Widget on Structure Summary pages and link to the corresponding external resource. If multiple experimental values are available for a measurement type, a range is listed.

Users can search for PDB entries with particular binding affinity in these databases using a new Advanced Search option. Any available information from BindingDB and BindingMOAD can also be included in custom tabular reports.

The External Ligand Annotation Widget for PDB entry 1hwk. Data in orange widgets on the RCSB PDB site are gathered from external resources.

Creating Tabular Reports

The Generate Reports pull-down menu on the Structure Hits tab offers different options for viewing a set of PDB entries. In addition to viewing a collage of structure images, users can create:

• A customized table of combinations of fields, including experi- mental, structural, and non-structural data; references to sequence databases (UniProtKB, Pfam), domain information (CATH, SCOP); literature (PubMed); and ontology terms (GO, MeSH)
• Pre-generated summary reports about structure, sequence, ligand, literature, and biological details
• Pre-generated experimental reports specific for X-ray or NMR structures from the Ligand Hits tab, a report that includes the ligand ID, image, formula, molecular weight, name, SMILES, and the PDB IDs for the related entries can be created.

Once a report has been created, the interactive table interface can be used to sort the table; refine results using an online filter; show/hide/move columns; change the number of results shown per page; and resize the table itself. Tables can be exported into Excel and CSV formats.

The Generate Reports pull-down menu. These reports offer convenient ways to view, export, and interact with query results.

New Data Distribution Summaries

RCSB PDB search results offer summary pie charts and summary links for standard characteristics of PDB entries that can be used to refine search results into subsets of interest. New charts for EC and SCOP classifications have been added to the list of available summary charts (resolution, release date, experimental method, polymer type, organism, taxonomy).

These drill-down options, or 'faceted search' options, 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. Any combination of categories is possible: users can quickly select the high resolution entries from a structure type search; human-related entries from a sequence search; or the most recently released entries resulting from a chemical component search.

Charts can also be "hidden" for users who only want to view individual entries.

Distribution summaries can be used to quickly browse and refine search results.

New Ligand Summaries

Users can toggle between a static image and a 3D Jmol view with the Ligand Image Widget.Ligand Summary Pages provide information about all of the entries found in the wwPDB's Chemical Component Dictionary. Similar to Structure Summary pages for PDB entries, widgets organize and highlight data on the page.

The Chemical Component Summary widget provides an overview of the structure, including name, identifiers, synonyms, and SMILES and InCHI information. A Related Entries widget links to all PDB entries where the ligand appears as a polymeric residue, a free ligand, or both. The Related Ligands widget links to summary pages for similar ligands and stereoisomers, and automatically enters the ligand in the RCSB PDB's Chemical Structure Search to build a search for a structurally similar ligand.

The Links widget lets users explore information related to the same chemical component at external resources (BindingDB, HIC-Up, PDBeChem and more) and the RCSB PDB's Ligand Expo. These pages can be accessed by performing a ligand search, selecting a ligand from a PDB entry's Structure Summary page, and from the Ligand Hits tab for query results.

Web Services

Web Services help software developers build tools that interact more effectively with PDB data. Instead of storing coordinate files and related data locally, Web Services let software tools interact with the RCSB PDB remotely. Documentation for accessing the RCSB PDB's Web Services is available from the Tools Widget in the left hand menu.

RESTful services exchange XML files in response to URL requests. RESTful search services return a list of IDs for Advanced Search and SMILES-based queries. RESTful fetch services return data when given IDs, including PDB entity descriptions, ligand information, third-party annotations for protein chains, and PDB to UniProtKB mappings. SOAP Web Services are also available.

Improvements are being made based on community feedback. Please let us know if there are website options that you think should be offered as a web service.