Searching and Browsing for PDB Structures
The Search Tab on the new RCSB PDB site offers many different ways of accessing the structures contained in the PDB archives.
The Advanced Search allows for simple queries based on structure summary items, keywords, structure/sequence features, ligands, biology & chemistry items, materials/methods, primary publication, and IDs (PDB, PubMed, Swiss-Prot, GenBank, PIR). These searches can be run in a variety of combinations to produce either very specific or very general results.
The Latest Release option displays images and summary information for structures added to the archives in the most recent update.
Forms are available to search specifically by sequence or ligand structure.
Unreleased structures can be searched by ID, title, authors, and sequence (when available).
The Queries tab shows all searches performed during the current web session. The results of these searches can also be retrieved.
Several simple text-based search options are also available on every page of the new site. Users can search the PDB archives using specific PDB IDs, keywords, or authors; run text searches on the static webpages; or search the archives and static webpages at the same time.
Browsers are available to navigate structures using classifications from Gene Ontology, EC nomenclature, source organism, disease, genome, SCOP, and CATH. Users can explore each category's hierarchy, view the number of associated PDB structures, and search for specific related structures. For example, the Disease Browser can be used to look at diseases involving the nervous system, such as fragile X syndrome and Tay-Sachs Disease. Selecting a disease of interest (e.g., Alzheimer Disease) will return all of the structures known to be associated with that disease.
For all searches, the resulting list of structures can be sorted, downloaded, used to create a tabular report (e.g., citation or sequence information), or further refined by combining the search with another query.
RCSB PDB Focus: Help systems for searching the PDB, depositing structures, and more
Electronic help desks and an integrated help system are available to support users navigating the RCSB PDB.
The help system (accessible through each button) launches into a separate browser window for accessing the help information and the website at the same time. It offers detailed topics (including Getting Started, Download Files, Search/Browse the Database, and Results), an index, glossary, and a search engine.
firstname.lastname@example.org answers questions about the deposition and annotation process at the RCSB PDB. Support pages at deposit.pdb.org include a file deposition and release FAQ, an overview of software tools, and tutorials for using ADIT, pdb_extract, the Validation Server, and Ligand Depot.
email@example.com responds to requests relating to the navigation of the RCSB PDB. Questions about searching, reporting, and using all of the resources available from the RCSB PDB should be sent to this address.
A narrated demonstration is available to help users explore the new features of the website. This short tutorial provides an excellent overview for searching, navigating, generating reports, visualizing structures, and browsing PDB data.
Enhanced Structural Genomics Portal
The RCSB PDB offers online tools, summary reports, and target information related to structural genomics at sg.pdb.org.
Information and links are provided for the structural genomics initiatives located worldwide, including reports for each center that provide target lists, target status progress, targets in the PDB, and sequence redundancy analyses.
Databases that track the progress of protein studies are available. TargetDB contains information about the progress of the production and solution of structures. PepcDB extends the content of TargetDB with status history, stop conditions, reusable text protocols and contact information collected from the PSI Centers.
A tool is also provided to explore the distributions of functions found among structural genomics structures, PDB structures, genomes, and homology models. This functional coverage can be examined according to Enzyme Classification, Gene Ontology (Biological Process, Cell Component, or Molecular Function) and Disease.
A paper describing the methodology of this tool has been published: Lei Xie and Philip E. Bourne (2005) Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Comput Biol 1(3): e31
Access statistics are given below for the RCSB PDB website at www.pdb.org.