How well are protein structures annotated in secondary databases?
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.
Rother
Kristian
K
Berlin Center of Genome-Based Bioinformatics (BCB), Institute of Biochemistry at the Charité, Humboldt Universität Berlin, Berlin, Germany. kristian.rother@charite.de
Michalsky
Elke
E
Leser
Ulf
U
D000595:Amino Acid Sequence; D030562:Databases, Protein / Q000592:standards*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011643:Publishing / Q000592:standards
D011506:Proteins