The role of structural bioinformatics resources in the era of integrative structural biology

Gerard J. Kleywegt EBI-EMBL

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Biologists today have an arsenal of three-dimensional imaging tools, modelling techniques and bioinformatics methods at their disposal to explore the molecules and processes of nature at a range of spatial scales and temporal resolutions. Integrative structural biology involves the collection and integration of these diverse pieces of structural and experimental data. Such approaches are increasing the reach and impact of structural biology and are crucial for enabling knowledge discovery in biomedical research

The structural biology and bioinformatics fields face two major challenges in regards to integration. Firstly, to integrate three-dimensional structural data obtained using a wide range of experimental techniques that span a continuum of spatial scales, from atomic to cellular (as illustrated in the figure). Secondly, for the structural data to be useful beyond the scope and lifetime of the project in which they were collected, it is vital to link together disparate bioinformatics resources and to provide useful, usable, accurate and up-to-date annotation about sequence, function, taxonomy, chemistry, genetic variation, etc.

In this paper, we briefly describe the history and status of the two prime archives in structural biology, the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), and present some of the on-going efforts at the Protein Data Bank in Europe (PDBe; http://pdbe.org) to address the challenges associated with the integration of structural and other data and information.

The scales of structural biology and their relationship to the currently available archives (EMDB and PDB): from the atomic details and interactions in a binding site to the cellular context of molecular machines, illustrated using the ribosome as an example.