IUCr activities

Open letter

To: Commission on Biological Molecules, IUCr

We, the undersigned, would like to request a revision of the IUCr policy on publication and deposition of data from crystallographic studies of biological macromolecules (Acta Cryst. A45, 658 (1989). It is our intention that if the policy gets revised, the new rules will be communicated to granting agencies and to scientific journals, in order to be universally accepted.

The current policy has been implemented on the basis of the discussions which had taken place a decade ago. In the meantime, there has been an incredibly rapid increase in the rate of determination of 3D structures of biomacromolecules, as reflected by the deposition of a new structure in the Protein Data Bank (PDB), on average, every five hours. Unfortunately, in parallel, an increasing proportion of depositors take advantage of the PDB's policy of allowing structures to be kept 'on hold' for up to a year after coordinate deposition. Consequently, as many as 45% of newly deposited structures are not available when the relevant papers are published.

When the issue of deposition was debated by the community ten years ago, the time needed to solve a macromolecular structure was often measured in years, and was rarely less than one year. The time needed for detailed analysis of such structures was also fairly long. The one-year hold on coordinates was therefore instituted to allow the authors to reap the fruit of their tremendous investment of time and effort. Due to recent advances in protein expression and purification, crystallization procedures, X-ray instrumentation, and computer software, the time needed to solve a structure is often shorter than the allowed hold period. In light of such developments, it is very difficult to justify withholding coordinates for any period once the paper has been published.

Biomolecular structure analysis has indeed succeeded in bringing 3D structures to the forefront of molecular biological research. This success has expanded both the interest in and utility of the information being deposited in the PDB. The molecular modeling community has grown and evolved considerably due to the expansion of this source of experimental data. The value of the data rests in their availability to the broader community. Methods are continuously being developed to analyze new structures and their relationships to the collection of existing structures. New uses for these data, such as statistical potentials for folding and threading calculations, and interface recognition tools, are evolving rapidly. No single research group can fully exhaust this wealth of information. The value of the resource grows proportionally to the timeliness of the data and to the number of scientists who have access to them. 3D structural information is also a crucial link elucidating the role of a translated region of a DNA sequence of unknown function.

We feel most strongly that the time has come to change the rules of deposition so as to ensure that the coordinates are released concomitantly with publication of the paper(s) describing the structure. We are convinced that without access to the coordinates, the structures cannot be utilized for comparison with other proteins, for theoretical analysis or, more and more importantly, for drug design. We propose that coordinates deposited at the PDB should be marked as either "for immediate release" or "to be released upon publication". We also recommend that the maximum hold for primary data, i.e., X-ray structure factors, and NMR-based restraints, be reduced from 4 years to 1 year. These changes would bring macromolecular crystallography into line with the requirements of other fields, such as gene sequencing, which have never allowed extended hold periods.

I would like you to print this petition in the IUCr newsletter. As discussed by us, this should be treated as a personal initiative at this time. If I find sufficient support, I will then submit the petition to the Commision on Biological Macromolecules of IUCr. Support (or opposition) messages should be sent to me (A. Wlodawer) at Macro-molecular Structure Lab. NCI-FCRDC, P.O. Box B Frederick, MD 21702, wlodawer@ncifcrf.gov, FAX: (301) 846-6128.

Alexander Wlodawer