The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.

The Protein Structure Initiative’s Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI’s high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology.

The Protein Data Bank (PDB) is the repository for three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive is free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and general audiences to understand biological phenomenon at a molecular level. Analysis of this structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included.

On behalf of the worldwide Protein Data Bank (wwPDB), we are responding to the commentary in your April issue entitled "Overhauling the PDB" (Nat. Biotechnol. 25, 437–442, 2007). We consider that the commentary fails to recognize the realities of dealing with complex biological macromolecular structural data, and with the equally complex and diverse communities who have a long history of working with these data.The wwPDB1 was formed to represent these international users and to ensure that the archive is kept to a uniform standard that enables the effective use and exchange of data content. The PDB archive consists of the flat files distributed via FTP (file transfer protocol). The term 'PDB' does not refer to the websites, browsers or database query engines developed by wwPDB partners. The wwPDB has not reengineered the PDB, nor is the term 'Brookhaven Protein Data Bank' appropriate, as Brookhaven's management of the PDB archive ended in 1998.In creating the wwPDB, we deliberately separated the PDB archive from the views of the data. The members of wwPDB have each created different instantiations of the same data. The resultant websites created by the the Research Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular Structure Database (MSD) at the European Bioinformatics Institute (Hinxton Hall, UK) and PDBj (Osaka University, Japan) each provide different services and views on the PDB data. Each database uses schemas that are in some manner derived from the macromolecular Crystallographic Information File (mmCIF), and are designed to satisfy particular search and retrieval requirements. None is put forward as a standard and each takes a different approach to data cleaning, normalization for integrity and denormalization for fast transaction services.The members of wwPDB are well aware of the complexities and inconsistencies in the PDB data. The PDB archive contains experimental data that have, until recently, not always been collected consistently. It includes data from new experimental techniques as they emerge, from many different contributing laboratories and from high-throughput structural genomics centers. The wwPDB has worked to remediate these data, and now all 42,000 entries have been corrected for errors in sequence, chemical components, nomenclature, citations and more. The wwPDB website (http://www.wwpdb.org/) provides information about the progress of this remediation project with the complete corpus available for community review2.Beyond remediation of the PDB archive, we have updated the rigor of our annotation practices to avoid introducing new errors in the future. All current databases derived from the PDB archive are loaded with preremediated data and have problems with data uniformity. This will be rectified as the remediated PDB passes from the test phase into full production over the next few months.The mmCIF was created under the auspices of the International Union of Crystallography (IUCr) as a dictionary of terms that describes the crystallographic experiment and the results3. The dictionary was extended to include terms for nuclear magnetic resonance and electron microscopy as defined by experts in these fields. This PDB Exchange Dictionary4 was created in full collaboration with structural biologists and computer scientists and represents a very detailed vocabulary for structural biology.The mmCIF was evolved from the small molecule CIF format5, which necessitated the creation of a new dictionary definition language (DDL). The semantics of the DDL provide the necessary details, such as category containers with natural key identifiers, semantic definitions and examples, data types with regular expressions, controlled vocabularies, boundary values, subclasses, aliases and versioning. In addition, directed relationships of the parent-child or foreign key types are described between common identifiers. These semantics permit the precise definition, validation and exchange of data. The use of this information makes it possible to perform largely automated transformations of the underlying data into different concrete formats—PDB, mmCIF or PDBML (an extensible markup language (XML) format developed by the wwPDB members6 as a direct translation of mmCIF)—to program application programming interfaces (APIs)7 and to remodel this information in various database schemas6. The mmCIF dictionary has been referred to as an ontology of terms for experimental structure determination8. The term 'ontology' currently implies a more specific set of modeled relationships, some of which are not present in our data dictionary.We also take issue with the assertion by Ross King and colleagues that data organization in our data dictionary, or any domain dictionary for that matter, should dictate the logical and physical organization of our database systems. Although the simple regular tabular organization of mmCIF simplifies the relational mapping of PDB data, each of the wwPDB groups has created a logical design and physical implementation that suits requirements of its particular web resources. The commentary authors refer to standard normalization techniques (that is, the third normal form (3NF)) to describe the design of the 'logical model' in a particular normal form. Universally, the 'physical model' that is then implemented does not necessarily have any particular form. Physical database implementations address issues of performance and maintenance using the logical model as the underlying basis. The authors have mixed the meanings of a logical model design with the implementations within the wwPDB websites.Finally, we certainly agree that the PDB should have a standard data representation, although a well-designed ontology plays less of a role than that championed by King and his coauthors. Even so, the legacy requirements of our community and the dynamics of changing a global resource require that it be developed over time and in collaboration with our diverse user base. Anything less is a gross underestimation of the current usage and impact of PDB data.

cAMP-binding domains from several different proteins were analyzed to determine the properties and interactions of this recognition motif. Systematic computational analyses, including structure-based sequence comparison, surface matching, affinity grid analysis, and analyses of the ligand protein interactions were carried out. These analyses show distinctive roles of the sugar phosphate and the adenine in the cAMP-binding module. We propose that the cAMP-binding regulatory proteins function by providing an allosteric system in which the presence or absence of cAMP produces a substantial structural change through the loss of hydrophobic interactions with the adenine ring and consequent repositioning of the C helix. The modified positioning of the helix in turn is recognized by a protein-binding event, completing the allostery.

In recognition of the growing international and interdisciplinary nature of structural biology, three organizations have formed a collaboration to oversee the newly formed worldwide Protein Data Bank (wwPDB; http://www.wwpdb.org/

The PDB has created systems for the processing, exchange, query, and distribution of data that will enable many aspects of high throughput structural genomics.

The 2 Å crystal structure reported here of the collagen-like model peptide, T3-785, provides the first visualization of how the sequence of collagen defines distinctive local conformational variations in triple-helical structure.

•The PDB is the first, community-driven, open-access digital archive in biology.•The data in the PDB are highly curated.•The wwPDB is an international partnership that manages the archive.•The wwPDB agrees on all standardization, processing, and dissemination policies.•Storing data and methods in a standardized way supports data reproducibility.The global Protein Data Bank (PDB) was the first open-access digital archive in biology. The history and evolution of the PDB are described, together with the ways in which molecular structural biology data and information are collected, curated, validated, archived, and disseminated by the members of the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org). Particular emphasis is placed on the role of community in establishing the standards and policies by which the PDB archive is managed day-to-day.

A symposium celebrating the 40th anniversary of the Protein Data Bank archive (PDB), organized by the Worldwide Protein Data Bank, was held at Cold Spring Harbor Laboratory (CSHL) October 28–30, 2011. PDB40's distinguished speakers highlighted four decades of innovation in structural biology, from the early era of structural determination to future directions for the field.

Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules. Since then, the number, size, and complexity of structural models have continued to grow, reflecting the productivity of structural biology. Managed by the Worldwide PDB organization, the PDB has been able to meet increasing demands for the quantity of structural information and of quality. In addition to providing unrestricted access to structural information, the PDB also works to promote data standards and to raise the profile of structural biology with broader audiences. In this perspective, we describe the history of PDB and the many ways in which the community continues to shape the archive.

The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85 000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data.Highlights► Current number of PDB entries is predicted to increase 1.5-fold by the end of 2017. ► The structures deposited in the PDB are growing in complexity. ► 3DEM is an emerging method for determining structures of large assemblies. ► Protein–nucleic acid complexes drive the growing number of nucleic acid structures.