Colin,
Speaking as someone who has one foot in small molecule crystallography
and the other in macromolecular, I have to say that attitudes are
completely different, and that there are good reasons for this. A PhD
student or junior postdoc in a macromolecular lab may have spent the
last three (or more) years cloning, expressing. purifying and
crystallizing a protein, and it is very likely that three or more groups
elsewhere in the world are working on the same target. Even if the
organisms are different, usually only one group will be able to publish
in a high-profile journal, so being scooped is a major worry and happens
frequently, even when all concerned are completely honest. A single
small molecule structure is a very much smaller part of the average
chemical PhD which often involves dozens of structures, and a couple of
duplicated structures will have little influence on the future career of
the PhD student.
Releasing the PDB hold on a structure just before submitting the paper
has something to be said for it. I would like to do this more often, but
it is usually vetoed by paranoid biological co-authors. Even if one is
providing the competition with a good MR model, at least they will have
to cite it.
George
On 04/19/2012 03:09 PM, Colin Groom wrote:
It has always struck me as something of a surprise that pre-publication review
of structures in protein-land
differs so significantly from small molecule-land. One of the activities
of the CCDC is to supply pre-release
CSD structures to referees, using a simple, automated system to
establish that the requestors are referees.
This avoids the need for any involvement of the depositor or journal and
allows a centralised record to be kept
as to who saw which structures and when (although, to my knowledge, we
have never needed to refer to this).
In 2012, requests have averaged at about 5 a day, but the real figure
is probably much higher, as some journals
provide this facility themselves. The sense I get from the
small-molecule community is that they (we) have a
great degree of well placed trust and see real value in pre-publication
review of structures, not just papers -
I'm sure this is true for the overwhelming majority of the
macromolecular world too.
Colin
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi.com
Sent: 19 April 2012 13:54
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
This is off course a valid point. A desperate graduate student faking a
structure risks his or hers career and reputation, while an anonymous
referee, "borrowing" someone else's results gets away without any risk
of being caught. Besides making the name of the reviewer public, I see
other options:
1) submit the coordinates and structure factors to the pdb to get a
priority date as has been suggested before. Many journals require
anyways a pdb code before acceptance of the paper. One could even
publish this priority date in the paper in the footnote where the pdb
code is mentioned.
2) require from referees a conflict-of-interest-statement that they, or
close colleagues are not working on the same or a very similar
structure. If an author gets the impression that he may have been
scooped by a less-ethical referee, he could ask the journal to verify
that the referees of his rejected paper were not involved in the
accelerated publication. If it turns out that a referee has made a false
statement this would clearly constitute fraud and a reason for
repercussions.
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Jobichen Chacko
Sent: Thursday, April 19, 2012 2:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear All,
Here comes the problem of blind reveiw, the authors are always at the
receving end to share all there data, results and now the full
cordinates to an unknown person, just trusting the journal editor. Why
don't the journals think about making the name of the reviewer also
public.
Eventhough the persons advocated giving the cordinates, there were cases
of holding the paper for reveiw for few months and finally rejecting it,
while a very close article appeared as accelerated publn within few
weeks of rejection of the original paper. Refer to the previous
discussion on fake structure.
Again it depends on how close you are towards the acceptance. Also
hesitation to give away your cordiantes without any guarantee of
publishing it in that journal cannot be considered as a big sin,
especially if someone's graduation is depend on a single paper.
Jobi
On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul
<m.kvansa...@latrobe.edu.au> wrote:
Dear CCP4BBlers,
I was wondering how common it is that reviewers request to have a copy
of the PDB coordinate file for the review purpose. I have just been
asked to supply this by an editor after several weeks of review, after
one of the reviewers requested a copy.
Not having ever been asked to do this before I feel just a tad
uncomfortable about handing this over...
Your opinions would be greatly appreciated.
Best wishes
Marc
Dr. Marc Kvansakul
Laboratory Head, NHMRC CDA Fellow
Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci
Bld 4, Kingsbury Drive, Melbourne, 3086, Australia
T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
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