Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

Abstract

Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain “hybrid” or “integrative” structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms. Here we present the development of data standards and a prototype system for archiving I/H models. The data standards provide the definitions required for representing I/H models that span multiple spatiotemporal scales and conformational states, as well as spatial restraints derived from different experimental techniques. Based on these data definitions, we have built a prototype system called PDB-Dev, which provides the infrastructure necessary to archive I/H structural models. PDB-Dev is now accepting structures and is open to the community for new submissions. Vallat et al., describe the data representation and prototype system for archiving structural models of biological macromolecules computed by integrative/hybrid modeling. The PDB-Dev prototype system enables the deposition, archiving and dissemination of integrative structural models in a standard form.