PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models

1 Aug 2019

Essential mechanisms in biology frequently involve large macromolecular assemblies (or machines). In favorable cases, their structures can be determined by X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy or electron microscopy (3DEM) alone, culminating in deposition of atomic structural models (with x, y, z atomic coordinates) into the global PDB archive (PDB; pdb.org). Many such biological machines are, however, poorly suited to single experimental method approaches. Researchers are increasingly forced to combine various experimental data and information from measurements and computational analyses to generate “hybrid” or “integrative” structural models of macromolecular assemblies. PDB-Dev is a prototype archiving system for structural models obtained through integrative/hybrid (I/H) methods. Structural characterization of many complex macromolecular assemblies is increasingly carried out using I/H methods, where a combination of complementary experimental and computational techniques is used to determine the structure. The structural models obtained through I/H methods are collected, archived, and disseminated to the public through PDB-Dev. The system currently consists of integrative/hybrid models that follow the specifications defined in the I/H methods dictionary, which is a modular extension of the PDBx/mmCIF dictionary. These include atomistic models, as well as multi-scale models, consisting of different coarse-grained representations