Hi Joel and Jaime - very nice to hear from you. I hope everything is going
well in Rehovot.
Proteopedia is the natural place to put comments etc. However it might
look more natural if there was more info there in the first place - ie if
people gave more explanation about the significance of thei
16-May-2014
Dear Patrick,
Proteopedia [http://proteopedia.org] uses exactly the same style for
referencing published material.
Proteopedia allows for the easy insertion of Pubmed and DOI references by only
requesting from the user to enter the Pubmed or DOI ids. We have extended the
same softwa
2014-05-15 9:53 GMT-03:00 Colin Nave :
> Of course exponential growth can’t go on forever – the hidden point behind
> my question.
>
A nice example from another biological database is Swissprot. It had an
exponential-like growth until 2009, and now it's somewhat linear:
http://web.expasy.org/doc
: [ccp4bb] PDB passes 100,000 structure milestone
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.
How about this utopia.. Imagine PD
So, a bit like "Fold-it" but with actual data? :-D
Dr David C Briggs PhD
http://about.me/david_briggs
On 16 May 2014 06:19, "Pavel Afonine" wrote:
>
> What about structures that are obviously wrong based on inspection of the
>> density, but no one has bothered to challenge yet? The TWILIGHT dat
> 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.
>
How about this utopia.. Imagine PDB has two versions: one is the original
data an
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 odditi
ng of the feedback by the rest of the community
would sort all problems out, provided there is enough participation.
Jose
-Original Message-
From: CCP4 bulletin board on behalf of Zachary Wood
Sent: Thu 5/15/2014 7:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB passes 10
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 T
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
con
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
ind
On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart 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
>
>
>
> Ceterum censeo structurae Murthius delendati erunt.
>
>
>
> (Marcus Tullius Raaijmakers)
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Joel
> Sussman
> *Sent:* Donnerstag, 15. Mai 2014 16:01
> *To:* CCP4BB@JISCMA
is currently under testing. Perhaps
>> this is the sort of thing that could work for structural data?
>>
>> cheers
>> Martyn
>>
>> From: Ethan A Merritt
>> To: CCP4BB@JISCMAIL.AC.UK
>> Sent: Wednesday, 14 May 2014, 19:22
>> Subject: Re:
oard [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joel
Sussman
Sent: Donnerstag, 15. Mai 2014 16:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
15-May-2014
Dear Martyn
Proteopedia's (http://proteopedia.org) goal goes well beyond just
education - i
] 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 t
the wider biological community.
all the best
Martyn
From: Zachary Wood
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, 15 May 2014, 14:47
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
Adding to Tim’s comment, I would not expect a tremendous
From: Ethan A Merritt
mailto:merr...@u.washington.edu>>
To: CCP4BB@JISCMAIL.AC.UK<mailto: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
ww.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:
ttp://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 To:
>
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
: [ccp4bb] PDB passes 100,000 structure milestone
A logarithmic plot of cumulative entries to the PDB is approximately linear and
shows a growth rate of about 15% per year. That means it doubles in size about
every 5 years at current growth rate.
Roger Rowlett
On May 15, 2014 4:23 AM, "Colin
. Perhaps this is the
sort of thing that could work for structural data?
cheers
Martyn
From: Ethan A Merritt
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
y. If we know the coefficients,
> we can work out when the PDB takes over the present universe. This would be
> time to retire.
> Can anyone do this?
> Thanks
> Colin
>
>
> From: James Holton [mailto:jmhol...@lbl.gov]
> Sent: 14 May 2014 16:19
> To: ccp4bb
> Subje
Hello,
I also agree that the right order of things would be the journals
taking action (i.e. retracting and commenting on why), then informing
the pdb which structures are associated with a retraction - for the
simple reason that very likely many readers take conclusions in
made-up public
__
From: Jon Agirre <mailto:jon.agi...@york.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, 14 May 2014, 14:28
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
249GB? That's a whole lot of DVDs!
On 14 May 2014 14:08, MARTYN
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
The policy doesn't say you can "supersede" someone else's entry.
It says you can deposit your own version, if you have a publication.
Then there will be two bogus structures instead of one. Pretty soon
the PDB will start to look like one of the cr
A little "loophole" that might make everyone happy can be found here:
http://www.wwpdb.org/policy.html
search for "A re-refined structure based on the data from a different
research group"
Apparently, anyone can supersede any PDB entry, even if they weren't the
original depositor. All they n
t;>
>>>> *From:* Jon Agirre
>>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>>> *Sent:* Wednesday, 14 May 2014, 14:28
>>>> *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
>>>>
>>>> 249GB? That's a whole lot of DVDs!
>>>>
>>>>
>>>> On 14 May 2014 14:08,
s each - am I calculating that wrong?
Maybe room for a 'making of' feature
;)
*From:* Jon Agirre
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Wednesday, 14 May 2014, 14:28
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
249GB? That&
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
On Wed, May 14, 2014 at 10:53 AM, Mark Wilson wrote:
> As for the meaning of integrity, I'm using this word in place of others
> that
> might be considered more legally actionable. A franker conversation would
> likely more clearly draw the line that we're wrestling with here.
>
The reference t
Hi Nat,
I agree that journals should be doing the heavy lifting here, for the
reasons that you note. I also want to be clear that I believe the PDB is a
crowning achievement of transparency and open access in the sciences,
which is one reason that I am so concerned about this issue. I am in no
way
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 stru
On Wed, May 14, 2014 at 10:26 AM, Mark Wilson wrote:
> Getting to Eric's point about an impasse, if the PDB will not claim the
> authority to safeguard the integrity of their holdings (as per their
> quoted statement in Bernhard's message below), then who can?
I think this may in part boil down
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
>
t;>
>>>>
>>>>
>>>>
>>>>
>>>> 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
ld be clearly marked.
Debasish
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark
Wilson
Sent: Wednesday, May 14, 2014 12:27 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
Hi Tim,
Getting to Eric&#x
;>> 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.
nally 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>*
>>>>>
>>>>>
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
>
t;>>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.UK<https://mail.google.com/mail/?view=cm&fs=1&tf=1&to=CCP4BB@JISCMAIL.AC.UK>]
>> *On Behalf Of *mesters
>
014 7:15 AM, MARTYN SYMMONS wrote:
>> I reckon it's two box sets of 25 discs each - am I calculating that wrong?
>> Maybe room for a 'making of' feature
>>
>> ;)
>>
>> ------------
>> *From:* Jon Agirre
>&
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 milest
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