PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models
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
Instruct-ERIC workshop on Computational Approaches in Integration of Structural Biology Techniques
On October 8 – 10, the Institute of Biotechnology of the Czech Academy of Sciences organised an Instruct – ERIC workshop on Computational Approaches in Integration of Structural Biology Techniques.
The 2019 Nobel Prize in Chemistry
Is awarded to John Goodenough, M. Stanley Whittingham and Akira Yoshino “for the development of lithium-ion batteries”.
The Nobel Prize in Physiology or Medicine 2019
is awarded jointly to William G. Kaelin Jr, Sir Peter J. Ratcliffe and Gregg L. Semenza “for their discoveries of how cells sense and adapt to oxygen availability.”
The Nobel Prize in Physics 2019
is awarded ”for contributions to our understanding of the evolution of the universe and Earth’s place in the cosmos”, with one half to James Peebles “for theoretical discoveries in physical cosmology” and the other half jointly to Michel Mayor and Didier Queloz “for the discovery of an exoplanet orbiting a solar-type star.”