On the prompt update of literature references in the Protein Data Bank

Updating literature references in the Protein Data Bank is discussed.

Abstract

Updating literature references in the Protein Data Bank is discussed.

One of annoying and potentially serious problems encountered during analysis of the macromolecular structures deposited in the Protein Data Bank (PDB) is the difficulty of finding where the research that resulted in the creation of some of the deposits was published. Conversely, although release of the coordinates upon publication of the relevant papers is now the law of the land, it is often difficult for the PDB to know that publication has taken place, since they have to search the whole literature for a specific PDB code. Typically, if the title of the future publication indicated during coordinate deposition differs from the final one, PDB has no way to know that the relevant paper has been published. Thus, many structures are not immediately released upon publication if the authors themselves do not promptly notify the PDB that their paper is already out.

I would like to make a simple suggestion that might help to rectify both problems. It should not be very difficult for a journal to generate a message to be sent to the PDB when a paper that refers to a newly deposited structure is actually published. ‘Publication’ would mean that any version of the paper becomes available to the readers, whether preliminary or final, depending on the editorial policy. If all journals that publish macromolecular structures would adhere to this recommendation, both problems mentioned above would become moot. Since the IUCr journals (mostly Acta Crystallographica Section D, Acta Crystallographica Section F and IUCrJ) publish a large fraction of papers that report new macromolecular structures, it would be particularly appropriate if they would spearhead such a policy.