TWILIGHT database, PDBREDO database, ... what else I forgot to name? I wonder why it should be under different brands and names, and not just be where it belongs to - the PDB?!
Back in 2005 when I (and colleagues) started re-refining the entire PDB (to test phenix.refine, mostly) and seeing oddities (by now well documented in the above mentioned debases and related publications) I felt very excited about starting a databases of curated structures, but thinking a bit it appeared strange and unnatural to have a "parallel" version of PDB. Pavel On Thu, May 15, 2014 at 11:23 AM, Nat Echols <[email protected]>wrote: > That is an extraordinary case, and it certainly took a huge amount of > work. What about structures that are obviously wrong based on inspection > of the density, but no one has bothered to challenge yet? The TWILIGHT > database helps some, if that counts, but it doesn't catch everything. > > -Nat > > > > On Thu, May 15, 2014 at 10:48 AM, Patrick Shaw Stewart < > [email protected]> wrote: > >> >> I may be missing something here, but I don't think you have to rebut >> anything. You simply report that someone else has rebutted it. Along the >> lines of >> >> Many scientists regard this published structure as unreliable since a >> misconduct investigation by the University of Alabama at Birmingham has >> concluded that it >> was, "more likely than not", faked [1] >> >> [1] http://www.nature.com/news/2009/091222/full/462970a.html >> >> >> >> >> >> >> On 15 May 2014 18:00, Nat Echols <[email protected]> wrote: >> >>> On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart < >>> [email protected]> wrote: >>> >>>> It seems to me that the Wikipedia mechanism works wonderfully well. >>>> One rule is that you can't make assertions yourself, only report >>>> pre-existing material that is attributable to a "reliable published >>>> source". >>>> >>> >>> This rule would be a little problematic for annotating the PDB. It >>> requires a significant amount of effort to publish a peer-reviewed article >>> or even just a letter to the editor, and none of us are being paid to write >>> rebuttals to dodgy structures. >>> >>> -Nat >>> >> >> >> >> -- >> [email protected] Douglas Instruments Ltd. >> Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK >> Directors: Peter Baldock, Patrick Shaw Stewart >> >> http://www.douglas.co.uk >> Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034 >> Regd. England 2177994, VAT Reg. GB 480 7371 36 >> > >
