Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

By Andrej Sali, Helen M. Berman, Torsten Schwede, Jill Trewhella, Gerard J. Kleywegt, Stephen K. Burley, John L. Markley, Haruki Nakamura, Paul D. Adams, Alexandre M. J. J. Bonvin and 28 more. 2015

175 citations recorded by the source corpus.

Summary Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?

Subfields: Molecular Biology

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Citations in the corpus

The SWISS-MODEL Repository—new features and functionality (2016, methodology): “the mmCIF model dictionary extension currently being developed in the context of the wwPDB task force on hybrid modeling (33).”
Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XII (2017, methodology): “Data-assisted or hybrid modeling, in which low-resolution experimental data are combined with computational methods, is becoming increasing important for a range of experimental data, including NMR, chemical cross-linking and surface labeling, X-ray and neutron scattering, and electron microscopy.(2”
The Cambridge Structural Database (2016, background): “We expect to see a continued push towards the federation of databases containing molecular structures (Sali et al., 2015) and the development of links between repositories.”
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. (2016, methodology): “to reproduce the docking, as recommended in the “Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop” (Recommendation 1) [25].”
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures (2021, background): “netic resonance (NMR), 3D electron microscopy (3DEM), small-angle scattering (SAS), chemical crosslinking, or integrative/hybrid methods (I/HM), 3D structural models of large macromolecular systems can be determined (1,2).”
Blind testing of cross‐linking/mass spectrometry hybrid methods in CASP11 (2016, methodology): “Most importantly, many protein targets are elusive to X-ray crystallography or NMR spectroscopy, because they cannot be isolated with the required purity, are insoluble, or do not crystal-lize.14 However, many experimental methods are still able to collect valuable, structural data on these targets.”