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Structural Databases of Biological Macromolecules

  1. Margaret J Gabanyi,
  2. Helen M Berman

Published Online: 17 SEP 2012

DOI: 10.1002/9780470015902.a0005252.pub2

eLS

eLS

How to Cite

Gabanyi, M. J. and Berman, H. M. 2012. Structural Databases of Biological Macromolecules. eLS. .

Author Information

  1. Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA

Publication History

  1. Published Online: 17 SEP 2012

Abstract

A biological macromolecule's function is determined by the chemical and physical characteristics of its three-dimensional (3D) shape, or ‘structure’. For this reason, knowing the structure of a biomolecule is very helpful if we want to be able to understand living systems and disease. The Protein Data Bank (PDB) began as an archive of the structural data available about biological macromolecules. The advances made in all technologies have been mirrored in further development of the PDB and in the structural speciality and structural characteristic databases that have also evolved. New resource portals such as the Protein Structure Initiative (PSI) Structural Biology Knowledgebase (SBKB) also collect all available genomic, structural, and functional information together to reduce the time needed to obtain the latest information on structurally determined proteins. This article will describe selected structural databases and resources available to the public today.

Key Concepts:

  • Structural information about proteins at the atomic-level can lead to an explanation of its role in living systems.

  • The Protein Data Bank archive is the sole provider of primary structural data of biological macromolecules worldwide.

  • The four members of the worldwide protein data bank consortium, the RCSB PDB, PDBe, PDBj and BMRB, maintain the PDB archive and provide tools for exploring and understanding the structural entries.

  • Other value-added databases further classify derived structural information by combining the structural and/or biological aspects of a biomolecule.

  • Meta-portals such as the Structural Biology Knowledgebase integrate all available genetic, structural, functional, and experimental information for all structurally determined proteins to enable a better understanding of sequence–structure–function relationships.

Keywords:

  • structural biology;
  • databases;
  • crystallography;
  • nuclear magnetic resonance;
  • electron cryomicroscopy;
  • structural genomics;
  • structural proteomics