My impression is that it's the case of "hot" structures NOT being checked
carefully. A while ago, after wrong (unrefined or poorly refined) structures of
Ras and Rubisco were published it became customary to not accept structures if
the R (Rwork at the time, Rfree was introduced later) wasn't below 0.25
together with proper fit to Ramachandran plot. Later Rfree was introduced and
another measure of caution helped to filter out wrong structures. In the last
few years several "hot" structure were allowed to be published (in Science,
Nature and Cell, of course) with horrensdous agreement R-factor, the
publication being justified solely, I suppose, based on their "hotness". (as I
recall the MacKinnon structure of the K-channel was the first in the series).
There is of course a case for difficult, most interesting and "hot" structures,
to be published in prestigious journals but they should be checked very
carefully, sometimes with other (additional) measures than the standard ones.
It's for the hot journals to work harder on refereeing those articles.
Boaz
----- Original Message -----
From: William Scott <[EMAIL PROTECTED]>
Date: Saturday, December 23, 2006 22:19
Subject: Re: [ccp4bb]: Retraction of ABC transporter structures - were there
warning signs?
To: [email protected]
> *** For details on how to be removed from this list visit
> the ***
> *** CCP4
> home page
> http://www.ccp4.ac.uk ***
>
>
>
>
> David J. Schuller wrote:
> > *** For details on how to be removed from this list
> visit the ***
> > *** CCP4
> home page
> http://www.ccp4.ac.uk ***
> >
> >
> > On Sat, 2006-12-23 at 13:32 -0500, Arun Malhotra wrote:
> >
> >> I was shocked to see the retraction in yesterday's issue of
> Science (Dec
> >> 22, 2006) of several ABC transporter structures and papers
> from the
> >> Chang lab, including three published in Science. The
> retraction says
> >> that the structures have the wrong hand and topology due to an
> >> "in-house" program that inverted the signs on the anomalous pairs.
> >>
> >> I have no expertise in ABC transporters, but were there
> warning signs in
> >> the structures? Were red flags raised by PDB or the other
> servers such
> >> as EDI, EDS, etc.? Looking at some of these papers, these are low
> >> resolution structure and I see very high R/Rfree, but there
> must have
> >> been other signs of problems as well.
> >>
> >> In the past few years, there have been almost no structures
> retracted>> due to gross errors and the checks being used by
> structural biology
> >> community seemed to working quite well - what can we learn
> from this
> >> tragic and sad error ?
> >>
> >
> > One thing we can learn is that a high-profile journal
> reporting on this
> > fiasco
> (http://www.sciencemag.org/cgi/content/full/314/5807/1856 Science
> > 22 December 2006:Vol. 314. no. 5807, pp. 1856 - 1857 DOI:
> > 10.1126/science.314.5807.1856), after having accepted three
> such botched
> > structures for publication, can find no room to criticise
> itself and
> > other high-profile journals. I believe the race between
> Science, Nature
> > and other top journals to get the hottest, sexiest articles has
> > contributed to their overlooking the solidity of the
> underlying work.
> >
>
>
>
> It sounds like an honest mistake, and it is not clear to me that the
> journal is at fault (unless they picked incompetent
> reviewers). The real
> question is whether this happens more frequently, but perhaps
> only the
> "hot" structures get double-checked. It is also asking a lot of the
> reviewers (and therefore the journal) to pick up on a mistake
> that the
> authors themselves presumably gladly would have done themselves
> if it had
> been more obvious.
>
> Again, maybe the best thing is to provide pdb, Fobs, exptl
> phases and maps
> to the referees. I do this now. At least one referee
> thanked me for it.
>
> It's also probably a good idea to use more than one software
> suite to
> reproduce the phasing and refinement, and check the answer with
> a SA
> composite omit map and/or EDEN for consistency. (EDEN has a phase
> perturbation function that is helpful.) Consistency
> doesn't equal truth,
> but if two similar programs give widely disparate results, it is
> a tipoff
> that something might be seriously amiss, even if the numerical
> statisticsdon't scream out that there is a problem.
>
>
>
>
>
>
>
Boaz Shaanan, Ph.D.
Associate Professor
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
