An analysis of the Protein Data Bank in search of temporal and global trends

Motivation: Biological databases, with their rapidly ex panning contents, a re indispensable tools in the quest to understand more about biological fun ction. However, a serious riser of a database that comprises a large collec tion of data, collected over a long period, will likely be struck by the in consistency in reporting individual items of data. This paper takes a criti cal look at the Protein Data Bank (PDB) to explore the seriousness of the p roblem in one particular data set and to explore the implications to those actively engaged in comparative analysis of these data. Results: Averaged over the complete corpus, the stereochemical quality of a tomic models has, in the past few years, moved towards ideal values. At the same time, there are inconsistencies in how data are reported. Water conte nt is not reported consistently and the percent of data collected when repo rting the high-resolution shell varies, detracting from the value of resolu tion as a yardstick for assessing the quality of a structure. A more detail ed analysis of these inconsistencies is hampered by the lack of machine-rea dable experimental data. To the riser of macromolecular structure data, thi s suggests that structural details beyond the standard quality measures of resolution and R value should be considered when using coordinate sets for further derivation or in inferring biological function. To the curators of the PDB, this suggests the need to capture more of the experimental dam ass ociated with the experiment in a way that permits straightforward parsing.