I’m afraid I don’t agree with Quyen - I do of course agree with the value of orthogonal methods (binding assays plus site-directed mutation of the residues involved in the binding site springs to mind in the case of ligand structures).
Specifically, a competitor should not be reviewing your paper in the first place. He or she should not have been invited by the editor, and if invited, should have declined the invitation straight-away.
I have almost always requested structure factors and coordinates when reviewing a structure paper, and they have always been provided without any questions or problems.
I plan to continue asking for this in all future papers I review, and will refuse to review the paper if the authors do not provide them.
When submitting a paper, I always try to provide the structure factors and coordinates upon submission as supplementary files not to be published, if the option is there.
I also think the pdb should take a more active role in rooting out at least the most clearly erroneous structures, we need participation by the journals, pdb and reviewers.
Which brings me to another point: have any “structures” been published in predatory journals yet and submitted to the pdb? As these journals will accept anything virtually un-reviewed, only the pdb can prevent those structures contaminating the database.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
> On 23 Jan 2016, at 15:42, Jurgen Bosch <[log in to unmask]> wrote:
>
> I agree with Quyen on both points. If you want to get your questionable structure published you better anticipate all questions a reviewer may have and stick them into the supplement in the first submission. Or add them as additional files for reviewer, which is often an option.
> Orthogonal methods to X-ray crystallography - aka biochemistry or other biophysical experiments supporting your opinion have to be added. I'm thinking ITC, SPR, MST, enzyme kinetics, mass spec etc.
>
> In general it is wise to try to disprove your own result before trying to publish it,
>
> Jürgen
>
> ......................
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab: +1-410-614-4894
> Fax: +1-410-955-2926
> http://lupo.jhsph.edu
>
> On Jan 23, 2016, at 08:41, Quyen Hoang <[log in to unmask]> wrote:
>
>> I have mixed feelings about the idea of providing referees access to model coordinates and the corresponding reflections. As a referee, couple occasions I wished that I had access to the data, but my concerns were resolved after the authors provided the omit and difference maps contoured as I requested. I didn't request for the model and data because I felt that I had no right to demand the authors to trust me that I wasn't their competitor trying to solve the same structures, or know someone who does. If I put myself into the authors' position, I would feel uneasy sending my unpublished model and data to an anonymous person. I also felt that as a referee, it wasn't my job to analyze data from which the reported results derived. In the examples that BR mentioned, I wonder if the erronous modeling of the ligands would have been uncovered had the reviewers asked for a simple omit map?
>>
>> Cheers,
>> Quyen
>>
>> Sent from my BlackBerry 10 smartphone.
>> From: Jrh
>> Sent: Saturday, January 23, 2016 2:00 AM
>> To: [log in to unmask]
>> Reply To: Jrh
>> Subject: Re: [ccp4bb] questionable structures
>>
>> Dear James, Dear Colleagues,
>> There is one more thing we can all do, namely when asked to referee articles with crystal structures, ask the journal to provide access to the authors' diffraction data and coordinates that are the bedrock of the words of the article.
>>
>> Recently I learnt that there is 'Peer reviewers openness initiative' described here :-
>> http://rsos.royalsocietypublishing.org/content/3/1/150547
>> This article and PRO initiative has a broad coverage and our field is very good in the respects that we have our crystal structure databases with very good user access. Our usual practices during refereeing are not as good as they could be; in my experience i have to ask the journal editor for the diffraction data and coordinates. Having done so the editor and authors have, except in one case, responded promptly with these. Maybe even glad of the keen interest!
>>
>> The concern you would have perhaps of not having time to repeat the analyses of the authors is dealt with in the article I cite above; see section 'Reviewers concerns'.
>>
>> Yours sincerely,
>> John
>>
>> On 22 Jan 2016, at 22:18, James Woo <[log in to unmask]> wrote:
>>
>>> What a ‘lively debate’ it is! As Herman said, the author should do something to their ‘bias interpretation’ model, retracting it from pdb and correct in their paper. But for the structure-dominated paper, things may not be that simple and easy. Because every other biochemical or genetic data are used by the author to support their model, if the model is fundamentally incorrect, let alone other part of the paper. It is not just the artificial water or ligand there, but it is the author’s attitude towards to the science. At this point, I fully understand the feeling of BR.
>>>
>>> There is one question about the oligomeric states of small molecules, like c-di-gmp, c-di-amp, or cGAMP (CDNs). 1, If these molecules are dimer or oligomer in their crystals, does this mean they are prone to adopt dimer or oligomer in solution? 2, If one enzyme or receptor can degrade or bind monomeric CDNs only, does oligomeric state of these small molecules in solution affect their activity (degrading or binding ) dramatically? Thank you in advance!
>>>
>>>
>>> On 22 January 2016 at 04:35, Bernhard Rupp (Hofkristallrat a.D.) <[log in to unmask]> wrote:
>>> > “The consensus of these experts is clear that the quality of the data and the level of noise within the electron density map in the Salunke study preclude tracing peptide residues within the x-ray crystal structures.”
>>>
>>> > Isn’t this equivalent to what you suggest, albeit in more diplomatic language?
>>>
>>> Hmm….which part of ‘and it should not be in any data base’ was unclear? -> cf. continuation Herman
>>>
>>> >Also, I think your language of “wrong” is imprecise (and therefore wrong), as Adrian pointed out.
>>>
>>> You are correct. The statement is *imprecise* but pretty darn *accurate* ;-)
>>>
>>> BR
>>>
>>>
>>>
>>>
>>>
>>> From: Bernhard Rupp [mailto:[log in to unmask]]
>>> Sent: Thursday, January 21, 2016 2:56 PM
>>> To: Keller, Jacob
>>> Cc: [log in to unmask]
>>> Subject: Re: [ccp4bb] questionable structures
>>>
>>>
>>>
>>> Simple statement: "The structure model is is almost certainly wrong (to the point of 'beyond reasonable doubt') and it should not be in any data base."
>>>
>>> How to handle the rest of the paper depends on the degree of inference based on the flawed model. But I am not doing all the work for the editors ;-)
>>>
>>>
>>>
>>> BR
>>>
>>>
>>>
>>> On Thu, Jan 21, 2016 at 8:40 PM, Keller, Jacob <[log in to unmask]> wrote:
>>>
>>> BR:
>>>
>>>
>>>
>>> Not clear what more you would have wanted to the editor to write—what’s missing?
>>>
>>>
>>>
>>> Or were you commenting on the lack of concrete actions?
>>>
>>>
>>>
>>> JPK
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> -----------------------------------------------------------------
>>> Bernhard Rupp (Hofkristallrat a. D)
>>> 001 (925) 209-7429
>>> +43 (676) 571-0536
>>> [log in to unmask]
>>> [log in to unmask]
>>> http://www.ruppweb.org/
>>> -----------------------------------------------------------------
>>> The hard part about playing chicken
>>> is to know when to flinch
>>> -----------------------------------------------------------------
>>>
>>>
>>
|
