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Archiving of Integrative Structural Models

  • Helen M. BermanEmail author
  • Jill Trewhella
  • Brinda Vallat
  • John D. Westbrook
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1105)

Abstract

Integrative or hybrid structural biology involves the determination of three-dimensional structures of macromolecular assemblies by combining information from a variety of experimental and computational methods. Archiving the results of integrative/hybrid modeling methods have complex requirements and existing archiving mechanisms are insufficient to handle these pre-requisites. Three concepts important for archiving integrative/hybrid models are presented in this chapter: (1) building a federated network of structural model and experimental data archives, (2) development of a common set of data standards, and (3) creation of mechanisms for interoperation and data exchange among the repositories in a federation. Methods proposed for achieving these objectives are also discussed.

Keywords

Protein Data Bank Integrative/hybrid modeling methods PDBx/mmCIF Data standards Data exchange Structural biology federation 

Notes

Acknowledgements

This work was supported by NSF EAGER grant DBI-1519158. We thank our collaborators Andrej Sali and Benjamin Webb for their contributions towards the development of the I/H methods data dictionary and the PDB-Dev prototype system. We thank all our colleagues in the I/H methods Task Force and the members of the wwPDB for their help and support with this project.

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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Helen M. Berman
    • 1
    Email author
  • Jill Trewhella
    • 2
    • 3
  • Brinda Vallat
    • 4
  • John D. Westbrook
    • 5
  1. 1.RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayUSA
  2. 2.School of Life and Environmental SciencesThe University of SydneySydneyAustralia
  3. 3.Department of ChemistryUniversity of UtahSalt Lake CityUSA
  4. 4.RCSB, Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayUSA
  5. 5.RCSB Protein Data Bank, Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayUSA

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