wwPDB and the wwPDB Integrative/Hybrid (I/H) Methods Task Force announce the public release of a prototype system for depositing I/H structural models, PDB-Development (or “PDB-Dev”) at pdb-dev.wwpdb.org.
Structural characterization of complex macromolecular assemblies is increasingly being carried out using 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 tools.
PDB-Dev was established to make I/H models available to the broader biological research community. It incorporates recommendations published by the wwPDB I/H Methods Task Force (1). PDB-Dev was built based on a data dictionary that captures the details of I/H models including a variety of experimentally-derived spatial restraints and the modeling of multi-scale, multi-state, time-ordered ensembles. The dictionary is an extension of the PDBx/mmCIF dictionary used by the wwPDB to archive macromolecular structures.
Currently, three test cases covering a variety of features of the Integrative Modeling Platform software (IMP, 2) have been deposited to PDB-Dev, including the 7-piece Nup84 sub-complex of the nuclear pore complex from yeast (3), the yeast exosome complex (4), and the yeast mediator complex (5).
PDB-Dev has been announced in Structure:
PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models Stephen K. Burley, Genji Kurisu, John L. Markley, Haruki Nakamura, Sameer Velankar, Helen M. Berman, Andrej Sali, Torsten Schwede, Jill TrewhellaStructure 2017 25: 1317-1318 doi: 10.1016/j.str.2017.08.001
wwPDB Partnership is committed to encouraging development of methods for archiving and validating I/HM structural data, and has published a policy governing I/HM depositions and the PDB archive.
Creation of PDB-Dev and the I/H methods data dictionary were supported by NSF EAGER award number 1519158.
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