Next-generation deposition expectations for the PDB

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Next-generation deposition expectations for the PDB

Post by terwill » Mon Oct 17, 2011 5:27 pm

Notes on discussion by telephone on Diffraction Data Deposition Working Group (John Helliwell and Tom Terwilliger, 5th Sept, 2011)

JRH summarized the DDD WG meeting at the IUCR and plans for a workshop in 1 year, likely at the Bergen ECM meeting; possibly also at the ACA meeting.

JRH pointed out the key role of archiving raw data along with its interpretation in published literature. This data would include not only crystallographic data but also the data leading up to this stage (purification, crystallization). TT noted how the structural genomics community has developed approaches for gathering and recording this information.

TT noted several aspects of deposition that might be included in the DDD WG vision. One was the concept of changing the paradigm of macromolecular structure deposition. Currently the focus is on the interpretation, the PDB file containing a structure. The addition of the data was something of an afterthought. A new paradigm would be that the data are first, and are permanent. The original depositor's PDB file and any other information would then be recorded as a specific interpretation of the data.

A second concept was that interpretations of the data may change over time as methods improve, or (as JRH pointed out) when additional information becomes available. Such new interpretations could be preserved and be made accessible in the same way as the original interpretation of the data. This could include automated interpretations such as is being done by PDB-REDO at present. JRH noted that in chemical crystallography the idea of re-determination of structures with new approaches is well-established.

TT noted further that not only the result, but also the process used to determine a structure is of great importance in evaluating the interpretation of the data. Recording key aspects of this process, or at a minimum, recording sufficient information to allow a complete redetermination of a structure would be of great value. John noted that the copper plastocyanin paper [1] 20 years ago is a good example of carefully analysing how the method used can affect the interpretation of crystallographic data.

TT described how the Commission on Biological Macromolecules had decided to focus on the issue of "Next-generation deposition expectations for the PDB" and that TT was chosen to be the leader of this effort. The CBM plans to develop a position paper on the subject in the near future. JRH suggested that the CBM might prepare a report on a 6-month time scale so that this report could be included in the deliberations of the DDD WG.

[1] J. M. Guss, H. D. Bartunik and H. C. Freeman Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 Å resolution Acta Cryst. (1992). B48, 790-811 [ doi:10.1107/S0108768192004270 ]

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Re: Next-generation deposition expectations for the PDB

Post by IUCr3323 » Mon Oct 17, 2011 8:50 pm

Not exactly focused lines:

If diffraction data is going to be deposited, running scripts of the key stages of the X-ray structure determination can be deposited as well, into Protein Data Bank. All software developers with the fastest sweep of their sword will supply necessary lines into the code to produce this information aimlessly for the crystallographer who use this software. Something similar to the tutorials which is parallel with every software. This information will not be of exceptionally large volume, and initially can be submitted with the PDB deposition, but eventually MUST be submitted.
It will be very educational.

Felix Frolow.

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