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

ABSTRACT: 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, on 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?

SUBMITTER: Sali A

PROVIDER: S-EPMC4933300 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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

Sali Andrej A Berman Helen M HM Schwede Torsten T Trewhella Jill J Kleywegt Gerard G Burley Stephen K SK Markley John J Nakamura Haruki H Adams Paul P Bonvin Alexandre M J J AM Chiu Wah W Peraro Matteo Dal MD Di Maio Frank F Ferrin Thomas E TE Grünewald Kay K Gutmanas Aleksandras A Henderson Richard R Hummer Gerhard G Iwasaki Kenji K Johnson Graham G Lawson Catherine L CL Meiler Jens J Marti-Renom Marc A MA Montelione Gaetano T GT Nilges Michael M Nussinov Ruth R Patwardhan Ardan A Rappsilber Juri J Read Randy J RJ Saibil Helen H Schröder Gunnar F GF Schwieters Charles D CD Seidel Claus A M CA Svergun Dmitri D Topf Maya M Ulrich Eldon L EL Velankar Sameer S Westbrook John D JD

Structure (London, England : 1993) 20150618 7

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, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, an ...[more]

PMID: 26095030

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Project description:The societal challenges posed by a growing human population and climate change necessitate technical advances in plant science. Plant research makes vital contributions to society by advancing technologies that improve agricultural food production, biological energy capture and conversion, and human health. However, the plant biology community lacks a comprehensive understanding of molecular machinery, including their locations within cells, distributions and variations among different cell types, and real-time dynamics. Fortunately, rapid advances in molecular methods, imaging, proteomics, and metabolomics made in the last decade afford unprecedented opportunities to develop a molecular-level map of plant cells with high temporal and spatial resolution. The Plant Cell Atlas (PCA) initiative aims to generate a resource that will provide fresh insight into poorly understood aspects of plant cell structure and organization and enable the discovery of new cellular compartments and features. The PCA will be a community resource (www.plantcellatlas.org/) that describes the state of various plant cell types and integrates high-resolution spatio-temporal information of nucleic acids, proteins, and metabolites within plant cells. This first PCA initiative workshop convened scientists passionate about developing a comprehensive PCA to brainstorm about the state of the field, recent advances, the development of tools, and the future directions of this initiative. The workshop featured invited talks to share initial data, along with broader ideas for the PCA. Additionally, breakout sessions were organized around topics including the conceptual goals of the PCA, technical challenges, and community wants and needs. These activities connected scientists with diverse expertise and sparked important discussions about how to leverage and extend leading-edge technologies and develop new techniques. A major outcome of the workshop was that the community wishes to redefine concepts of plant cell types and tissues quantitatively. A long-term goal is to delineate all molecules within the cell at high spatio-temporal resolution, obtain information about interacting molecular networks, and identify the contribution of these networks to development of the organism as a whole. As a first step, we wish to create comprehensive cellular and subcellular biomolecular maps of transcripts, proteins, and metabolites, track the dynamic interactions of these molecules intra- and intercellularly, discern complete states and transitions of specialized cell types, and integrate these disparate data points to generate testable models of cellular function. Ultimately, the PCA initiative will have a substantial positive impact by empowering a broad, diverse group of scientists to forge exciting paths in the field of plant science, facilitating connections with interested stakeholders beyond the scientific community, and enabling new agricultural technologies for a sustainable future.

Dataset Information

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

Publications

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

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