Re: [ccp4bb] PDB passes 100,000 structure milestone
I agree with Martyn, Pubmed Commons could be a great model. I believe you have to be a published author to obtain an account. It might cut down on some of the spam/noise if the PDB adopted such a model for depositors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 7:29 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB passes 100,000 structure milestone
Adding to Tim’s comment, I would not expect a tremendous amount of spurious comments about a single PDB out of 100,000 unless there was a problem. Especially if the Pubmed Commons model was applied, and only depositors could comment. I would assume this would be very beneficial, given that we are conscientious professionals. Could actually be a great forum for authors to go a little deeper into specific approaches or problems that they had with a structure. Not all interesting details make it to the pub. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 9:39 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, isn't the ccp4bb a very good example that spam may not be such an issue for a discussion platform on structures in the PDB? There is a great variety of opinions, some to agree with, some to disagree, but all of them interesting and contributing, and I hardly remember a message I would classify as spam. And it all works without restraints. Best, Tim On 05/15/2014 03:21 PM, Zachary Wood wrote: I agree with Martyn, Pubmed Commons could be a great model. I believe you have to be a published author to obtain an account. It might cut down on some of the spam/noise if the PDB adopted such a model for depositors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 7:29 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG
Re: [ccp4bb] PDB passes 100,000 structure milestone
Dear Jaime and Joel, Perhaps an easier solution would be to get the PDB to put an obvious link on each entry directing the user to the Proteopedia site for discussion and additional details. I would personally prefer a comments/discussion section on the PDB page, but as long as one is easily accessible I would be happy. By the way, you guys are doing a great job, and I will now go officially register on your site so that I can be user 2,601 ;-) Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 10:00 AM, Joel Sussman joel.suss...@weizmann.ac.il wrote: 15-May-2014 Dear Martyn Proteopedia's (http://proteopedia.org) goal goes well beyond just education - it is aimed at Structural Biology and non Structural Biology Community and it would be pleased to be a forum for discussion of structures that are questionable. There are now over 2,600 registered users, who are contributing to Proteopedia, in over 50 different countries. Proteopedia has a special area for discussions related to each structure. To access it, you go to the structure's page, e.g. http://proteopedia.org/w/2x24 and click on the 'discussion' tab on the page's upper border. Everyone can read the comments there, and it will open a fully editable page for every registered user to add their comments on the structure and their full name will be listed below their comments. If you would like to contribute to this, we’d be pleased to welcome your input. Best regards, Jaime Prilusky Joel Sussman On 15May, 2014, at 7:29, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB passes 100,000 structure milestone
I agree with Nat. If you think a structure has a problem area, it is much easier to point it out to the users than to publish a rebuttal. Comments are easy. Simply state your observation. If you are wrong in your assessment, I am sure you will receive a fine education from the more learned individuals in our community. And since this pertains to the entire PDB, I do not see a lot spam/noise being produced on a single structure. I would suspect almost nothing will be said regarding the majority of the 100,000 structures. I am not aware of a ton of spam being produced on the publications in the Pubmed Commons. In fact, it saddens me that no one has said anything significant about my publications. I personally would prefer to limit the feedback to those who deposit structures (similar to how Pubmed Commons limits comments to authors). I believe that we as a community are the ones best positioned to police the database. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 1:00 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk 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
Re: [ccp4bb] PDB passes 100,000 structure milestone
Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 14, 2014, at 12:47 PM, Mark Wilson mwilso...@unl.edu wrote: Hi Tim, I agree with everything you've said about the importance of validation, but aren't we really talking about something different here? Users of structural information should of course be keeping a careful eye on validation reports. On the other hand, what possible reason is there for the PDB to continue to archive and offer for public use models whose fundamental integrity (rather than quality or reliability) are highly suspect? I hope that I'm not the only one who is frustrated that the page for 2HR0 is still available and unblemished by warnings. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1tf=1 to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or lessŠ.) valid entries only at the time of announcement. Cheers, BR Supplemental material: ³The PDB says it will remove the other ten structures only when editors at the journals in which they were originally published or the authors themselves retract them² *http://www.nature.com/news/2009/091222/full/462970a.html http://www.nature.com/news/2009/091222/full/462970a.html* ³With the support of the structural-biology community, the mission of the wwPDB is to safeguard the integrity and improve the quality of the PDB archive.² http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Not to be overly cynical, but http://tinyurl.com/pmupalt *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1 tf=1to=CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *mesters *Sent:* Mittwoch, 14. Mai 2014 14:42 *To:* CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to =CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of
Re: [ccp4bb] EDS server - R-value
Hi Jai, I had the same thing happen when I pulled up one of my lab's structures. It was twinned, and at least in the past the EDS did not handle twinning. Best regards, Z *** Zachary A. Wood, Ph.D. Assistant Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On Apr 4, 2014, at 4:07 AM, jai mohan wrote: Dear all, Sorry for the off-topic Question. I just tried to extract files *.* from EDS server for a PDB entry. The page tells us that There is no map available for this entry (), because our automatic script failed to produce an electron density map with an R-value (0.309) within 5 percentage points of the published one (0.165). If you are the author of this entry and wish to help us remedy this situation, please contact us. Back to EDS home page The reported R-value for the () PDB entry is 0.16 than how 0.309? could anyone please explain about this! Sincerely, S.M. Jaimohan, Ph. D
Re: [ccp4bb] On pKa of Aspartic acid
Hi Kevin, Hate to point this out, but under pH 7.0, the protonation state of water is not 50:50, and it is not a good acid. The H30+ concentration of pure water is 10^-7 Molar. In pure water (assuming 55.5 M) only 1:555,000,000 water molecules is in the protonated, charged state (H3O+). This is why when an enzyme uses water in its mechanism as a nucleophile, base, or acid, there is usually an acid/base catalyst or metal that protonates or deprotonates the water to 'activate it'. Best regards, Z *** Zachary A. Wood, Ph.D. Assistant Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On Feb 7, 2012, at 11:22 AM, Kevin Jin wrote: As we know, the pKa of water is 15.7. Under pH 7.0, its protonation should be 50/50. In this case, we may need to consider water in two formats: H2O vs. H3O+ When we say water as acid, it usually stands for H3O+ in chemistry. In chemical equation, H+ represents H3O+. In enzyme catalysis, water as a general acid sounds reasonable under pH 7.0. In some famous paper, water has been concluded as the general base (pKa 15.7) to deprotonate an alpha hydrogen (pKa ~ 22) or a hydrogen from a sp3 hybridized carbon (pKa ~36). This logic may need to be reconsidered. . Recently, I have read papers for pKa perturbation. I am also interested in the general base of Asp and Glu in enzyme catalysis. I will be very happy to read your paper in the future. Regards, Kevin Jin On Tue, Feb 7, 2012 at 3:48 AM, Deepak Oswal deepos...@gmail.com wrote: Dear colleagues, We have solved the crystal structure of a human enzyme. The pKa of a catalytically critical aspartic acid has increased to 6.44. It is hydrogen bonded (2.8 Angstroms) to a water molecule that is supposed to donate a proton during the catalysis. Can anybody help me a) interpret the significance of this increase in pKa of the aspartic acid from 3.8 to 6.44 in context with the catalysis? Is this advantageous or detrimental? b) How is pKa related to an amino acids’ ability to force a water molecule to donate a proton? c) At pH 7.4, the aspartic acid would be de-protonated irrespective of whether the pKa is 3.8 or 6.44; isn’t that true? d) Have similar increase in pKa values observed for aspartic acids before? I would be grateful if anybody could explain or comment on the above queries. Deepak Oswal
