The literature already contains quite a few papers discussing ligand-protein
interactions derived from low-resolution data, noisy data, etc. It's
relatively easy to take a low-quality map; dock the molecule willy-nilly
into the poorly defined 'blobule' of density, and derive spectacular
conclusions. However, in order for such conclusions to be credible one needs
to support them with orthogonal data such as biological assay results,
mutagenesis, etc. This is not limited to crystallography as such, and it's
the referee's job to be thorough in such cases. To the author's credit, in
*most* cases the questionable crystallographic data is supported by
biological data of high quality. So, even with the images, etc. - it's still
quite possible to be honestly mislead. Which is why we value biological
data.
Consequently, if one's conclusions are wrong - this will inevitably show up
later in the results of other experiments (such as SAR inconsistencies for
example). Science tends to be self-correcting - our errors (whether honest
or malicious) are not going to withstand the test of time.
Assuming that the proportion of deliberate faking in scientific literature
is quite small (and we really have no reason to think otherwise!), I really
see no reason to worry too much about the ligand-protein interactions. Any
referee evaluating ligand-based structural papers can ask to see an omit map
(or a difference density map before any ligand was built) and a decent
biological data set supporting the structural conclusions. In the case of
*sophisticated deliberate faking*, there is not much a reviewer can do
except trying to actually reproduce the claimed results.
On the other hand, the 'wholesale' errors can be harder to catch, since the
dataset and the resulting structure are typically the *only* evidence
available. If both are suspect, the reviewer needs to rely on something else
to make a judgement, which is where a one-page summary would come handy.
Artem
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Juergen Bosch
Sent: Saturday, August 18, 2007 12:20 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] The importance of USING our validation tools
Hi Mischa,
I think you are right with ligand structures and it would be very
difficult if not impossible to distinguish between real measured data
and faked data. You just need to run a docking program dock the ligand
calculate new structure factors add some noise and combine that with
your real data of the unliganded structure.
I'm not an expert, but how would one be able to detect say a molecule
which is in the order of 300-600 Da within an average protein of perhaps
40 kDa if it's true data or faked + noise ?
In Germany we have to keep data (data meaning everything, from clones,
scans of gels, sizing profiles to xray diffraction images etc.) for 10
years. Not sure how this is in US.
Juergen
Mischa Machius wrote:
>I agree. However, I am personally not so much worried about entire protein
>structures being wrong or fabricated. I am much more worried about
>co-crystal structures. Capturing a binding partner, a reaction
>intermediate or a substrate in an active site is often as spectacular an
>achievement as determining a novel membrane protein structure. The
>threshold for over-interpreting densities for ligands is rather low, and
>wishful thinking can turn into model bias much more easily than for a
>protein structure alone; not to mention making honest mistakes.
>
>Just for plain and basic scientific purposes, it would be helpful every
>now and then to have access to the orginal images.
>
>As to the matter of fabricating ligand densities, I surmise, that is much
>easier than fabricating entire protein structures. The potential rewards
>(in terms of high-profile publications and obtaining grants) are just as
>high. There is enough incentive to apply lax scientific standards.
>
>If a simple means exists, beyond what is available today, that can help
>tremendously in identifying honest mistakes, and perhaps a rare
>fabrication, I think it should seriously be considered.
>
>Best - MM
>
>
>
>
>On Sat, 18 Aug 2007, George M. Sheldrick wrote:
>
>
>
>>There are good reasons for preserving frames, but most of all for the
>>crystals that appeared to diffract but did not lead to a successful
>>structure solution, publication, and PDB deposition. Maybe in the future
>>there will be improved data processing software (for example to integrate
>>non-merohedral twins) that will enable good structures to be obtained from
>>such data. At the moment most such data is thrown away. However, forcing
>>everyone to deposit their frames each time they deposit a structure with
>>the PDB would be a thorough nuisance and major logistic hassle.
>>
>>It is also a complete illusion to believe that the reviewers for Nature
>>etc. would process or even look at frames, even if they could download
>>them with the manuscript.
>>
>>For small molecules, many journals require an 'ORTEP plot' to be submitted
>>with the paper. As older readers who have experienced Dick Harlow's 'ORTEP
>>of the year' competition at ACA Meetings will remember, even a viewer
>>with little experience of small-molecule crystallography can see from the
>>ORTEP plot within seconds if something is seriously wrong, and many
>>non-crystallographic referees for e.g. the journal Inorganic Chemistry
>>can even make a good guess as to what is wrong (e.g wrong element assigned
>>to an atom). It would be nice if we could find something similar for
>>macromolecules that the author would have to submit with the paper. One
>>immediate bonus is that the authors would look at it carefully
>>themselves before submitting, which could lead to an improvement of the
>>quality of structures being submitted. My suggestion is that the wwPDB
>>might provide say a one-page diagnostic summary when they allocate each
>>PDB ID that could be used for this purpose.
>>
>>A good first pass at this would be the output that the MolProbity server
>>http://molprobity.biochem.duke.edu/ sends when is given a PDB file. It
>>starts with a few lines of summary in which bad things are marked red
>>and the structure is assigned to a pecentile: a percentile of 6% means
>>that 93% of the sturcture in the PDB with a similar resolution are
>>'better' and 5% are 'worse'. This summary can be understood with very
>>little crystallographic background and a similar summary can
>>of course be produced for NMR structures. The summary is followed by
>>diagnostics for each residue, normally if the summary looks good it
>>would not be necessary for the editor or referee to look at the rest.
>>
>>Although this server was intended to help us to improve our structures
>>rather than detect manipulated or fabricated data, I asked it for a
>>report on 2HR0 to see what it would do (probably many other people were
>>trying to do exactly the same, the server was slower than usual).
>>Although the structure got poor marks on most tests, MolProbity
>>generously assigned it overall to the 6th pecentile, I suppose that
>>this is about par for structures submitted to Nature (!). However there
>>was one feature that was unlike anything I have ever seen before
>>although I have fed the MolProbity server with some pretty ropey PDB
>>files in the past: EVERY residue, including EVERY WATER molecule, made
>>either at least one bad contact or was a Ramachandran outlier or was a
>>rotamer outlier (or more than one of these). This surely would ring
>>all the alarm bells!
>>
>>So I would suggest that the wwPDB could coordinate, with the help of the
>>validation experts, software to produce a short summary report that
>>would be automatically provided in the same email that allocates the PDB
>>ID. This email could make the strong recommendation that the report file
>>be submitted with the publication, and maybe in the fullness of time
>>even the Editors of high profile journals would require this report for
>>the referees (or even read it themselves!). To gain acceptance for such
>>a procedure the report would have to be short and comprehensible to
>>non-crystallographers; the MolProbity summary is an excellent first
>>pass in this respect, but (partially with a view to detecting
>>manipulation of the data) a couple of tests could be added based on the
>>data statistics as reported in the PDB file or even better the
>>reflection data if submitted). Most of the necessary software already
>>exists, much of it produced by regular readers of this bb, it just needs
>>to be adapted so that the results can be digested by referees and
>>editors with little or no crystallographic experience. And most important,
>>a PDB ID should always be released only in combination with such a
>>summary.
>>
>>George
>>
>>Prof. George M. Sheldrick FRS
>>Dept. Structural Chemistry,
>>University of Goettingen,
>>Tammannstr. 4,
>>D37077 Goettingen, Germany
>>Tel. +49-551-39-3021 or -3068
>>Fax. +49-551-39-2582
>>
>>
>>
>
>
>---------------------------------------------------------------------------
-----
>Mischa Machius, PhD
>Associate Professor
>UT Southwestern Medical Center at Dallas
>5323 Harry Hines Blvd.; ND10.214A
>Dallas, TX 75390-8816; U.S.A.
>Tel: +1 214 645 6381
>Fax: +1 214 645 6353
>
>
>
--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
|
