Linked Life Data

17704562

Source:http://linkedlifedata.com/resource/pubmed/id/17704562

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
Pt 9
pubmed:dateCreated
2007-8-20
pubmed:abstractText
The genomics era has seen the propagation of numerous databases containing easily accessible data that are routinely used by investigators to interpret results and generate new ideas. Most investigators consider data extracted from scientific databases to be error-free. However, data generated by all experimental techniques contain errors and some, including the coordinates in the Protein Data Bank (PDB), also integrate the subjective interpretations of experimentalists. This paper explores the determinants of protein structure quality metrics used routinely by protein crystallographers. These metrics are available for most structures in the database, including the R factor, R(free), real-space correlation coefficient, Ramachandran violations etc. All structures in the PDB were analyzed for their overall quality based on nine different quality metrics. Multivariate statistical analysis revealed that while technological improvements have increased the number of structures determined, the overall quality of structures has remained constant. The quality of structures deposited by structural genomics initiatives are generally better than the quality of structures from individual investigator laboratories. The most striking result is the association between structure quality and the journal in which the structure was first published. The worst offenders are the apparently high-impact general science journals. The rush to publish high-impact work in the competitive atmosphere may have led to the proliferation of poor-quality structures.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
0907-4449
pubmed:author
pubmed:issnType
Print
pubmed:volume
63
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
941-50
pubmed:meshHeading
pubmed:year
2007
pubmed:articleTitle
Quality of protein crystal structures.
pubmed:affiliation
University of Iowa, Department of Biochemistry, Iowa City, IA, USA.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't