Short Communication

How well are protein structures annotated in secondary databases?

  1. Kristian Rother1,*,
  2. Elke Michalsky1,
  3. Ulf Leser2

Article first published online: 14 JUL 2005

DOI: 10.1002/prot.20520

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 60, Issue 4, pages 571–576, 1 September 2005

Additional Information

How to Cite

Rother, K., Michalsky, E. and Leser, U. (2005), How well are protein structures annotated in secondary databases?. Proteins: Structure, Function, and Bioinformatics, 60: 571–576. doi: 10.1002/prot.20520

Author Information

  1. 1

    Berlin Center of Genome-Based Bioinformatics (BCB), Institute of Biochemistry at the Charité, Humboldt Universität Berlin, Berlin, Germany

  2. 2

    Berlin Center of Genome-Based Bioinformatics (BCB), Institute of Computer Science, Humboldt Universität Berlin, Berlin, Germany

*Institute of Biochemistry at the Charité, Humboldt Universität Berlin, Monbijoustr. 2, 10117 Berlin, Germany

Publication History

  1. Issue published online: 15 AUG 2005
  2. Article first published online: 14 JUL 2005
  3. Manuscript Accepted: 8 FEB 2005
  4. Manuscript Revised: 25 JAN 2005
  5. Manuscript Received: 1 SEP 2004

Funded by

  • German Ministry of Education and Research (BMBF). Grant Number: 0312705B

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Keywords:

  • cross-references;
  • data quality;
  • database annotation;
  • databases;
  • protein structure

Abstract

We investigated to what extent Protein Data Bank (PDB) entries are annotated with second-party information based on existing cross-references between PDB and 15 other databases. We report 2 interesting findings. First, there is a clear “annotation gap” for structures less than 7 years old for secondary databases that are manually curated. Second, the examined databases overlap with each other quite well, dividing the PDB into 2 well-annotated thirds and one poorly annotated third. Both observations should be taken into account in any study depending on the selection of protein structures by their annotation. Proteins 2005. © 2005 Wiley-Liss, Inc.

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