“The Protein Data Bank (PDB) was established as the first open access repository for biological data, and the datasets it hosts have been invaluable to research in fundamental biology and the understanding of health and disease. Just this month, we witnessed the announcement of the AlphaFold2 results toward structure prediction, made possible thanks to the more than 170,000 freely accessible structures in the PDB which provided “training data” for the structure prediction software.
It was not always the case that such structural biology data were freely available, even upon journal publication. From the founding of the PDB in 1971 until the late 1980s, most journals did not require deposition of structures in a public database. A key moment was a petition, circulated in 1987 by a group of leading structural biologists, demanding that the data created be made openly available upon journal publication. This petition led to major journals adopting data deposition standards. In the early 1990s, the National Institute of General Medical Sciences (NIGMS) imposed similar requirements on all grantees.
The revolution in publishing made possible by preprints calls for a re-evaluation of data disclosure practices in structural biology. While journal review processes take weeks, months, or even years, preprints allow researchers to rapidly communicate their findings to the community. However, withholding access to PDB files that accompany preprints inhibits the progress towards scientific discovery which preprints can enable.
We pledge to publicly release our PDB files (and associated structure factor, restraint, and map files) with deposition of our preprints.
We encourage all structural biologists to also deposit raw data in appropriate resources (e.g. EMPIAR, proteindiffraction.org, https://data.sbgrid.org/, etc). …”