Safeguarding Structural Data Repositories against Bad Apples

Wladek Minor; Zbigniew Dauter; John R Helliwell; Mariusz Jaskolski; Alexander Wlodawer

doi:10.1016/j.str.2015.12.010

Safeguarding Structural Data Repositories against Bad Apples

Structure. 2016 Feb 2;24(2):216-20. doi: 10.1016/j.str.2015.12.010.

Authors

Wladek Minor¹, Zbigniew Dauter², John R Helliwell³, Mariusz Jaskolski⁴, Alexander Wlodawer⁵

Affiliations

¹ Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA. Electronic address: wladek@iwonka.med.virginia.edu.
² Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.
³ School of Chemistry, University of Manchester, Manchester M13 9PL, UK.
⁴ Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences and Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland.
⁵ Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.

Abstract

Structural biology research generates large amounts of data, some deposited in public databases or repositories, but a substantial remainder never becomes available to the scientific community. In addition, some of the deposited data contain less or more serious errors that may bias the results of data mining. Thorough analysis and discussion of these problems is needed to ameliorate this situation. This perspective is an attempt to propose some solutions and encourage both further discussion and action on the part of the relevant organizations, in particular the PDB and various bodies of the International Union of Crystallography.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Computational Biology / methods*
Data Accuracy
Data Mining
Databases, Protein / standards*
Models, Molecular
Protein Conformation
Proteins / chemistry*

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding