The RCSB Protein Data Bank: new resources for research and education

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher's PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.

Figure 1.

Top bar searching. This example shows several suggestions for the search term ‘virus’. In the Taxonomy category, the ‘Viruses’ link will return all entries in the virus superkingdom, even if the word ‘virus’ does not appear in the text of the entry. Conversely, entries with irrelevant matches for ‘virus’ (such as an occurrence in a related citation) are excluded. The searches with the most results are shown first, such as the hits for ‘Human immunodeficiency virus 1’ and ‘Influenza A virus’ under Organism. The ‘Molecule of the Month’ category offers related articles from PDB-101. Finally, a custom ‘Retrieve’ category provides easy access to all entries where the biological assembly represents the complete virus particle. Numbers in parentheses represent the number of entries that match a specific term, and text in brackets represents the name of a structural domain classification scheme or ontology. Search suggestions can be restricted to specific categories by selecting the ‘Author’, ‘Macromolecule’, ‘Sequence’ or ‘Ligand’ icon above the text search box. The default search is set to ‘All Categories’.

Figure 2.

Domain-based structural alignment database search results for PDB ID 1ZUP (30), a hypothetical protein and a putative nuclease. (a) The sequence is shown with different annotations, starting with the UniProtKB sequence at the top. Most of this sequence has been resolved (SEQRES) with ATOM records available in the PDB, with the exception of a region at the N-terminus and two short regions toward the C-terminus of the protein. SCOP provides an annotation of a single domain protein, the PDP software assigns two domains to this protein and Pfam detects a NurA domain motif. (b) The hits listed in the table show similarities to a NurA structure, as well as several endonucleases. (c) When viewing the details of the first alignment [1ZUP shown in orange and NurA domain of 2YGK (31) in cyan], one notices that several loop and helical regions are not conserved between the two structures, but the core is well conserved. Structural alignments are accessible from the 3D Similarity tab of any entry’s Structure Summary page.

Figure 3.

RCSB PDB Mobile. The left image shows the query results from a macromolecule name search for ‘porin’ on an iPhone. Basic information about each entry is displayed in the results list. Entry 3SY7 has been tagged (red asterisk) and entry 3SY9 (43) has been annotated (yellow note pad icon) in the MyPDB account of the user. Entry 3SY7 in the NDKMol viewer is shown on the right. Structures in the viewer can be rotated, translated and zoomed using finger gestures, and touching the camera icon captures an image. The menu at the bottom allows the user to switch to the search menu, run MyPDB queries, browse ‘Molecule of the Month’ articles or launch the 3D viewer.

Figure 4.

The top portion of an Author Profile displaying the structures associated with author W.A. Hendrickson is shown. Timelines can be sorted by deposition date and specific time ranges can be selected from the right hand menu. Author profiles can be bookmarked and shared.