Data Query, Reporting, and Access

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

• A new Gene View illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB protein chains (chosen from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.
• The average temperature (B) factor has been added to the Refinement Details section of the tabular report creation options.
• The website has been redesigned so that a new navigation menu at the top of the website replaces the traditional left-hand menu.

See the What's New page for more new features and examples.

Protein Feature View for UniProt ID P69905 showing the new Exon Structure track

RCSB PDB's Protein Feature View visually summarizes how a full-length protein sequence from UniProt 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.

The Protein Feature View was recently redesigned to improve readability and to add descriptions of protein function, subunit structure, domains information, and genomic exon structure.

Protein Feature View can be launched from the "Molecular Description" section of a Structure Summary page (see 2d5z) as well as by searching for a UniProt ID (P69905) or Gene Symbol (Hba1). These Protein View images can be exported as Scalable Vector Graphics (SVG) files.

The PDB to UniProt mapping is based on the data provided by the SIFTS project.

Structure Summary pages for X-ray crystal structures provide access to validation information based upon the recommendations of the wwPDB X-ray Validation Task Force:

• The "slider" graphic displayed on the page gives an indication of the quality of the determined structure as compared with previously deposited PDB entries using several important global quality indicators
• The full PDB Validation Report PDF, which contains the slider graphic and other information to provide an assessment of the quality of a structure and highlight specific concerns (visit the wwPDB for more information)
• A new PDF report containing Ramachandran plots created using MolProbity (version 4.02b). Ramachandran plots provide an independent method to evaluate the conformational quality of protein structures, and offer a visual representation of any outliers tabulated in the Validation Report PDF. For more information about MolProbity, see Chen et al. (2010) Acta Cryst D66:12-21.

Previously, Ramachandran plots were located on the Structure Summary Geometry tab, which has been retired. Additional validation data and statistics are available from the Structure Summary Links tab, including reports by WHAT_CHECK and PROCHECK.

Ramachandran plots for entry 1cbs as created by MolProbity.

Set up a MyPDB account to create a personalized version of the RCSB PDB that is accessible from any computer.

Use the MyPDB widget in the left-hand menu to create an account and then log in to access stored setting and functionalities:

• Saved Query Manager. Use MyPDB to store any type of structure search, such as keyword, sequence, ligand, and any composite query built with Advanced Search. These queries can be run at any time with the click of a button.  For example, users who frequently search for zinc finger motif using Advanced Search (Sequence Features>Sequence Motif=CX{2,4}CX{12}HX{3,5}H) can store the search in MyPDB, name it "zinc finger," and then run the query at any time.
• Stored searches can also be set to run with each update. Email alerts (weekly or monthly) will be sent when new PDB entries matching the search are released.
• Personal Annotations. Users can save personal annotations and notes on the Structure Summary tab of any PDB entry, and can add structures to a "favorites list". The Personal Annotations summary page provides easy access to all of these tagged structures and annotations.
• User Account. Personal information (name, email address, account password, country, user type) can be updated at any time. All MyPDB account information is kept private and secure.

Saved Query Manager Features.
A) After saving a search to MyPDB, name it by clicking on the words "User Query" providing a more descriptive label.
B) The manager can be used to change email notification settings, run queries, and delete saved searches.

Use the Transporter Classification Browser to find PDB's membrane transport proteins as organized by TC Database family (www.tcdb.org). The browser will autocomplete search terms with the matching classifications, and highlight locations on the tree.

RCSB PDB's Browse Databasefeature offers access to structures in the PDB archive using different hierarchical trees.

Browsers are available to find structures organized around the following classifications:

• Anatomical Therapeutic Chemical (ATC) Classification System from the WHO Collaborating Centre for Drug Statistics Methodology
• Membrane Proteins in the PDB are identified using the mpstruc database (Stephen White, UC Irvine), sequence clustering, and data derived from UniProt
• Protein Symmetry, as calculated for all protein complexes in the PDB, and updated weekly
• Trees for Biological Process, Cellular Component, and Molecular Function are organized using the Gene Ontology (GO) Consortium's descriptions for gene products. PDB IDs and corresponding chain IDs have been mapped to GO terms by the SIFTS initiative
• Enzyme Classification by name or partial/full EC number
• Transporter Classification from the Transporter Classification Database
• Source Organism using organisms found in NCBI Taxonomy 
• Genome Location of various organisms, using NCBI Genome and Entrez Gene
• MeSH (Medical Subject Headings) that appear in the entry's related PubMed abstract
• SCOP description of evolutionary and functional relationships from SCOP: Structural Classification of Proteins
• CATH clustering of proteins at four major levels from CATH: Protein Structure Classification

Click Browse from the top of every RCSB PDB page and then the desired Browser Tab to start searching.