Proteopedia has this - see https://proteopedia.org/wiki/index.php/Proteopedia:Comments_on_Published_Structures
Kay On Fri, 19 Jul 2019 17:42:33 +0000, Bonsor, Daniel <dbon...@som.umaryland.edu> wrote: >Would it be possible to add a public annotations section to the PDB, to allow >us to potentially flag/warn whoever downloads that particular structure, there >could be something wrong with it, such as wrong space group, no/poor density >fitting for ligand. Something similar to PubPeer maybe? > > >Daniel A. Bonsor PhD >Institute of Human Virology, >University of Maryland at Baltimore >725 W. Lombard Street N571 >Baltimore >MD 21201 > > >________________________________ >From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Patrick Loll ><pjl...@gmail.com> >Sent: Friday, July 19, 2019 1:17 PM >To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 > >The idea of contacting the editor (and/or author) is an excellent one, and >indeed the correct thing to do scientifically. However, I�m disillusioned: >I�ve been down this path before with a high-profile vanity journal, and while >the editors paid lip service to the notion that the record should be >corrected, in reality they led me on for the better part of a year, and got me >to write up detailed analyses of why the ligand positioning was not justified, >before eventually saying �no, we don�t see any need to publish a correction.� >I speculate that the journal prefers not avoid corrections, for fear that too >many corrections will make the journal a less desirable destination. > >> On 19 Jul 2019, at 11:23 AM, B�rbel Blaum <baerbel.bl...@intherabio.com> >> wrote: >> >> Hi Rhys, >> the reported B-factors for the �ligands� are all way below the reported >> B-factors for the protein chains, with the worst of the three complexes >> reporting unitless numbers 23.2 and 64.8, respectively, just to highlight >> *one* striking feature of the data collection and refinement table. So even >> with the limited info normally available to reviewers this table should have >> raised a red flag. After the re-refinement suggested by others, i.e. your >> own proper assessment of the crystallographic data, if you do not find >> noteworthy density you may want to contact the article�s editor with your >> results. If you work in this field, i.e. really care about this paper >> scientifically and you are not afraid to confront the authors you could >> suggest writing a comment/direct response article but in my opinion that >> would only make sense if you can be sure beforehand that it will be linked >> visibly to the actual paper, else it will be a waste of time. And don�t >> forget that just because one or some of the authors did a bad job at the >> crystallographic end other findings of the paper might still be solid � in >> collaborations often one author is unable to critically evaluate another >> author�s contribution and this would not be the first case were good >> synthetic or biological work is presented along with a bad crystal structure. >> By the way and a bit ironically this protein may have suffered bad >> crystallography/scientific practice before - I think it was one of the fake >> Krishna Murthy structures, right? The associated (now retracted) article I >> mean is here >> https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub >[https://ars.els-cdn.com/content/image/S00222836.gif]<https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub> >RETRACTED: Crystal structure of dengue virus NS3 protease in complex with a >bowman-birk inhibitor: implications for flaviviral polyprotein processing and >drug design - ScienceDirect - ScienceDirect.com | Science, health and medical >journals, full text articles and >books.<https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub> >www.sciencedirect.com >COMMUNIC Crystal Structure of Dengue Complex with a Bowman-Bir ro L. 1Center >for Macromolecular C f A 8 U T MCLM 244, Birmingham AL 35294-0005, USA >2Department of Biochemistry and Molecular Biology, Kansas University Medical >Center 3901 Rainbow Boulevard Kansas City, KS 66160- 7421, USA Dengue viruses >are members of the Flaviviridae and cause dengue fever Dengue fever and dengue >hemorrhagic ... > >> Kind regards, B�rbel >> --- >> B�rbel Blaum, PhD >> Inthera Bioscience AG >> Einsiedlerstrasse 34 >> CH-8820 Waedenswil >> Switzerland >> E-Mail: baerbel.bl...@intherabio.com >> Phone: +41 43 477 94 72-- >> >> >> >> Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> im Auftrag von "Manfred S. >> Weiss" <manfred.we...@helmholtz-berlin.de> >> Antworten an: "Manfred S. Weiss" <manfred.we...@helmholtz-berlin.de> >> Datum: Freitag, 19. Juli 2019 um 16:03 >> An: <CCP4BB@JISCMAIL.AC.UK> >> Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 >> >> Hi Rhys, >> >> all three structures are at modest resolution and they don't seem to >> be properly refined. At least they are all below average. I wonder >> how this paper made it past the referees. >> >> I haven't checked the paper, but there are ways and means how to >> deal with weakly bound ligands in the best possible way. One aspect >> is to improve the phases as much as possible without having the ligand >> present. This was obviously NOT done. Another way is to use the >> PANDDA approach, which relies on having many data sets available. >> I suppose that this was also not done. >> >> The best way to check is to delete the ligand and so some extensive >> refinement in order to remove the phase bias introduced by the >> ligand. Only then you can reliably assess whether something is there >> or not. >> >> Cheers, Manfred >> >> Am 19.07.2019 um 15:21 schrieb Rhys Grinter: >>> Hi All, >>> >>> I was chatting with a colleague during a recent synchrotron visit and >>> they'd recently come across some ligand/drug bound structures associated >>> with a paper recently published in a high impact factor journal. >>> >>> They had pulled the associated SFs from the PDB and found that the electron >>> density associated with these ligands didn't match that reported in the >>> paper and certainly wasn't sufficient to model the alleged ligand. >>> >>> I also pulled the structure factors and after refinement in the >>> presence/absence of the alleged ligand I also feel that the density present >>> does not warrant modelling of the ligand. >>> >>> I was hoping that the community might be able to give me an outside opinion >>> on these datasets (PDB IDs: 6MO0, 6MO1, 6MO2) and if the problem associated >>> with the data is verified, provide some advice on how to proceed. >>> >>> This isn't the first occasion I've seen ligand bound structures with >>> questionable density deposited in association with papers in well respected >>> journals. Despite improvements to validation I feel that this problem is >>> widespread. >>> >>> Best Regards, >>> >>> Rhys >>> >>> -- >>> Dr Rhys Grinter >>> NHMRC Postdoctoral Researcher >>> Monash University >>> +61 (0)3 9902 9213 >>> +61 (0)403 896 767 >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> >> >> -- >> Dr. Manfred S. Weiss >> Macromolecular Crystallography >> Helmholtz-Zentrum Berlin >> Albert-Einstein-Str. 15 >> D-12489 Berlin >> Germany >> >> >> Helmholtz-Zentrum Berlin f�r Materialien und Energie GmbH >> >> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren >> e.V. >> >> Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta >> Koch-Unterseher >> Gesch�ftsf�hrung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan L�ning, >> Thomas Frederking >> >> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >> >> Postadresse: >> Hahn-Meitner-Platz 1 >> D-14109 Berlin >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > >--------------------------------------------------------------------------------------- >Patrick J. Loll, Ph. D. >Professor of Biochemistry & Molecular Biology >Drexel University College of Medicine >Room 10-102 New College Building >245 N. 15th St., Mailstop 497 >Philadelphia, PA 19102-1192 USA > >(215) 762-7706 >pjl...@gmail.com >pj...@drexel.edu > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
