Abstract
Structures of many complex biological assemblies are increasingly determined using integrative approaches, in which data from multiple experimental methods are combined. A standalone system, called PDB-Dev, has been developed for archiving integrative structures and making them publicly available. Here, the data standards and software tools that support PDB-Dev are described along with the new and updated components of the PDB-Dev data-collection, processing and archiving infrastructure. Following the FAIR (Findable, Accessible, Interoperable and Reusable) principles, PDB-Dev ensures that the results of integrative structure determinations are freely accessible to everyone.
Highlights
Integrative structure determination is an approach to modeling the structures of biological systems based on information produced by multiple experimental and theoretical methods (Rout & Sali, 2019; Sali, 2021)
The library is freely available from the project GitHub repository. Modeling software, such as Integrative Modeling Platform (IMP; Russel et al, 2012) and HADDOCK (Dominguez et al, 2003), use python-ihm to read and write IHM-dictionary-compliant mmCIF files that are archived in Protein Data Bank (PDB)-Dev
We have described how the new set of data standards, supporting software tools and the different components of the PDB-Dev system provide the foundational infrastructure for archiving and disseminating integrative structures
Summary
Integrative structure determination is an approach to modeling the structures of biological systems based on information produced by multiple experimental and theoretical methods (Rout & Sali, 2019; Sali, 2021). The PDB archives multi-method structures that are based on one of the traditional methods (X-ray, NMR or 3DEM) used in combination with methods such as neutron diffraction or SAS. These multi-method structures contain only atomic coordinates and the different experiments are carried out on the same molecular system (for example NMR and SAS experiments carried out on the same molecular system). These multi-method structures currently archived in the PDB are a subset of integrative structures. We describe the different components of PDB-Dev and highlight recent improvements and updates
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