Archiving of Integrative Structural Models

Helen M Berman; Jill Trewhella; Brinda Vallat; John D Westbrook

doi:10.1007/978-981-13-2200-6_16

Archiving of Integrative Structural Models

Adv Exp Med Biol. 2018:1105:261-272. doi: 10.1007/978-981-13-2200-6_16.

Authors

Helen M Berman¹, Jill Trewhella^{2

3}, Brinda Vallat⁴, John D Westbrook⁵

Affiliations

¹ RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA. berman@rcsb.rutgers.edu.
² School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
³ Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
⁴ RCSB, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
⁵ RCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.

PMID: 30617834
DOI: 10.1007/978-981-13-2200-6_16

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

Publication types

Review

MeSH terms

Macromolecular Substances / chemistry*
Models, Molecular*
Molecular Biology*

Substances

Macromolecular Substances