This is the first time a journal has contacted me to tell me that one of the reviewers wants me to provide them with the pdb files (the unreleased coordinate files of the novel structures we are describing in the paper). I have never been asked to send a pdb file to a reviewer before ... all I needed to provide until now were tables with the structural statistics, pictures to illustrate the findings and the code names of the files after deposition in the Protein Data Bank (but not the files themselves as the Protein Data Bank keeps them secret and does not release them until the codes have been published by a journal first).
Is this common practice?
A pdb file (pdb=protein databank the file format of the public protein databank) is a set of coordinates describing a protein structure. It can be loaded into a variety of programs (such as Pymol) to provide an interactive 3D display of the protein.
The reviewer is asking for it because it is much easier to see structural features in interactive 3D form than in a static picture. The reviewer may be looking for something that isn't described in the paper, for example, how close your structure is to a homologous structure. The reviewer may simply want to see the features you describe for him or herself.
In any case, in almost all situations there is very little to lose by not sending the PDB file immediately. The experiments are done, the paper is written. It is unlikely you will be scooped at this point. Since the PDB file is going to be deposited in a public database anyway, intellectual property concerns probably don''t apply (but check with the appropriate people if this is a concern).
Dear Antonio,
me too, I have no idea what "pdb" means.
But I do a lot of reviews and I would never ask an author to provide any sort of raw data exceeding what is written in the paper.
If there were technical details that needed clarification, this could most likely be done in communication done by mail.
If your miraculous pdb-file contains any data relevant for intellectual property (IP), I'd strongly advise not to share it and try to solve any issue by sticking to the paper's content.
UPS! My bad ... I assumed only structural biologists would read and reply to my question.
I've edited the question to make this clearer.
A pdb file (pdb=protein databank the file format of the public protein databank) is a set of coordinates describing a protein structure. It can be loaded into a variety of programs (such as Pymol) to provide an interactive 3D display of the protein.
The reviewer is asking for it because it is much easier to see structural features in interactive 3D form than in a static picture. The reviewer may be looking for something that isn't described in the paper, for example, how close your structure is to a homologous structure. The reviewer may simply want to see the features you describe for him or herself.
In any case, in almost all situations there is very little to lose by not sending the PDB file immediately. The experiments are done, the paper is written. It is unlikely you will be scooped at this point. Since the PDB file is going to be deposited in a public database anyway, intellectual property concerns probably don''t apply (but check with the appropriate people if this is a concern).
This is a reasonably common request. The reviewer may also want the validation report which the PDB provides, which lists any geometric outliers and/or poor fits to density.
I agree with Jeffrey above. It's not common but I have asked (and been provided with) a PDB file before now. You have very little to loose, and the Journal would be absolutely livid if the reviewer subsequently abused it. Your PDB file would likely be released almost immediately anyway no?
Dear Antonio,
it all depends how "hot" your structure is. If it is something really novel and "big" - I would never send a pdb file, and actually there is no such obligation imposed by the journals. You can provide the extended validation report, which gives sufficient information about the quality of your model. Of course it is way easier to see your model to judge it, but unfortunately sometimes it can end up in hands of your direct competitor - something you would really like to avoid.
If your structure is not a huge advance, let's say there are already several homologues known, or you study the binding of some ligands, it is probably OK to send it, but again it is up to you. You can send a figure of a piece of your model with electron density, if there is a particular question from a reviewer.
Good luck with your paper,
Albert
I have often been invited to send in a PDF in lieu of a book by a reviewer. In fact, most publishers and agents ask for PDFs, rather than mailed manuscripts or books. This is the first I heard of a pdb file.
i am hearing this for the first time
i am sure of pdf but not pdb
- Badges
- Science topic
- Similar topics
- Social Science
- Media
- Journalism