A data dictionary for archiving integrative/hybrid models
Brinda Kizhakke Vallat, Benjamin Webb, John Westbrook, Andrej Šali, Helen Miriam Berman · Acta Crystallographica Section A Foundations and Advances · 2017
Structural characterization of complex macromolecular assemblies is increasingly being carried out using integrative and hybrid (I/H) methods. Traditional structure determination methods such as X-ray crystallography and NMR spectroscopy are generally insufficient for tackling such complex assemblies. Recently, methods have been developed that combine spatial restraints derived from a variety of complementary experimental techniques, including cryo-electron microscopy, small angle scattering, chemical crosslinking, mass spectrometry and other proteomics and bioinformatics methods. A feature of integrative modeling is that it allows for multi-scale, multi-state, and time-ordered ensembles, which are very different from the mono-scale atomistic models currently archived in the Protein Data Bank [1]. Our goal is to facilitate the archiving of I/H models so that they can be available to the broader biological research community. We have created a data dictionary that captures the details of I/H models including a variety of experimentally-derived spatial restraints and the modeling of multiscale, multi-state, time-ordered ensembles. The dictionary is an extension of the PDBX/mmCIF dictionary [2] used by the Protein Data Bank to archive macromolecular structures. The dictionary and supporting documentation are publicly accessible [3]. Creating an archive for I/H models is vital to the evolving structural biology community and the data dictionary is a critical step in this direction. This work is supported