The paper with this structure was published in the year 2008, following
which, the PI and coPIs who co-authored the paper would have submitted
grants using this information as preliminary data. It is possible some
of these grant applications may even have got funded at the expense of
other grants that had the good data. This is the not the first
instance, there have been papers/structures that have been retracted
after ten years of publication.
Is there any thing the funding agencies can do?
Sridhar
On 8/10/2011 3:50 PM, Dale Tronrud wrote:
> Oops! My bond length rmsd was 0.106 not 0.160 A. Still unacceptable
> but not quite as bad.
>
> Sorry,
> Dale Tronrud
>
> On 08/10/11 15:45, Dale Tronrud wrote:
>> I've made a quick look at the model and the paper - and it doesn't
>> need more than a quick look. The description of the model in
>> the paper sounds great. The problems in the model are clear. My
>> favorite is the quote "Trp-477 of PTH1R makes several van der Waals
>> contacts with Trp-339 and Lys-337 of G-beta-1 ...". They are "contacts"
>> all right. The distances between the 477:CH2 and 337:CE is 2.75 A
>> and between 477:NE1 and 339:CH2 is 2.26 A. There are many more.
>>
>> In general the geometry of this entire model is terrible. In
>> Table 1 the bond length rmsd is listed at 1.64 A and the bond angles
>> are 0.0078 deg! Perhaps one is to presume the numbers should be
>> swapped. In any case, the values I calculate for the model are
>> 0.160 A and 4.46 deg! Absolutely dreadful. The PDB header lists
>> the (swapped) values from the paper and then reports hundreds of
>> outliers.
>>
>> The tools proposed by the Validation Task Force should cause a
>> model like this to pop out clearly. Even the old tools show this
>> model is quite unreliable. We just have to use them.
>>
>> Dale Tronrud
>>
>> On 08/10/11 14:35, Jacob Keller wrote:
>>> On the surface it doesn't seem as bad as others, i.e., it does not
>>> seem to be a real fake--perhaps just a strong form of wishful thinking
>>> and creative density interpretation. I wonder what would be a good
>>> metric in which to establish a cutoff for present/not present in
>>> density. CC, maybe?
>>>
>>> Jacob
>>>
>>> On Wed, Aug 10, 2011 at 4:01 PM, David Schuller<[log in to unmask]> wrote:
>>>> Time to fuel up the gossip engines for the approaching weekend:
>>>>
>>>>
>>>> http://www.sciencedirect.com/science/article/pii/S096921260800186X
>>>>
>>>> RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to
>>>> the G-Protein Dimer Gβ1γ2
>>>> Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094
>>>> Structure 2QNS withdrawn.
>>>>
>>>> --
>>>> =======================================================================
>>>> All Things Serve the Beam
>>>> =======================================================================
>>>> David J. Schuller
>>>> modern man in a post-modern world
>>>> MacCHESS, Cornell University
>>>> [log in to unmask]
>>>>
>>>
>>>
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