Talk:Protein Data Bank

message: From the article: "The PDB is a key resource in structural biology and is critical to more recent work in structural genomics."  Some references here for work that uses the PDB in an interesting/important way would be good.
From the article: "Countless derived databases and projects have been developed to integrate and classify the PDB in terms of protein structure, protein function and protein evolution." Such as? Give some examples for the derived databases.
From the growth section: "The growth rate of the PDB has been the subject of fairly extensive analysis."  .. such as? this needs referencing, why was it subject to extensive analysis? where are these?
: I agree that these statements should be cited, I don't agree that a lack of citation is a reason to 'dumb down' the article. I don't think any structural biologists or crystallographers would have too much trouble accepting the above facts. Nevertheless, it seems Wikipedians are always willing to take it upon themselves to dumb down an article, rather than to educate themselves! I'll try to find some references for these facts (or at least some citeable examples) and re-instate them in the article. --Dan|(talk) 15:59, 23 May 2009 (UTC)
thread_title: More detail and references needed in history section

message: A new page Protein Data Bank (file format) is needed, which should cross link to Chemical file format and use also the proper Category:Chemical file format category. JKW 15:58, 8 April 2006 (UTC)
replies: text:  Initial Protein Data Bank (file format) created and anything related to format discussions on the Protein Data Bank should be moved to this page. JKW 11:20, 22 April 2006 (UTC)
replies: text:  I agree we should move junk from the file format section on this article to the file format article. --Dan|(talk) 13:41, 7 March 2008 (UTC)
thread_title:  [[Protein Data Bank (file format)]] needed 

message: I believe all the concerns above have been considered in the revision of the article today.  I think every thing is referenced, though sometimes one reference covers an entire paragraph.--Christopher King (talk) 03:59, 5 January 2009 (UTC)
replies: text: See my comment above in the section #More detail and references needed in history section. --Dan|(talk) 16:00, 23 May 2009 (UTC)
thread_title: Rewrite

message: There needs to be more information about PDB Identifiers. I am a hobbyist editor and not a biochemist so I do not know the origins of the identifier or who started this naming format. Who came up with the identifier design and method? Who gets to decide what proteins get added to the series?
Are there "reserved regions" of the identifier for certain content, or are new sequences just added serially as it arrives from researchers?
As far as I can determine, it is a base-36 naming system using numbers 0-9 and letters A-Z. If it is limited to just four powers, as currently stated in the text of this article, that is only 1,679,616 possible PDB entries. 
Does anyone seriously believe that there will never be more than 1.7 million protein structures found and mapped, across the entire history of life on the planet?
It would make more sense if additional powers/digits can be added as needed. A fifth digit will allow 60,466,176 total patterns, and sixth digit alows 2,176,782,336 patterns, etc.
DMahalko (talk) 23:00, 20 May 2009 (UTC)
replies: text: Hey DMahalko, your understanding of the code is correct. I don't know how it was decided on, but that is how it is. In the past authors picked their own codes. These days they are automatically assigned by the submission software. The limited number of codes has been discussed on and off over the years on the PDB-L mailing list https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l (where I'm sure someone would answer any questions you have on the above. You may also like to search (or even improve) the unofficial PDB FAQ here http://pdbwiki.org/index.php/PDB_FAQ HTH --Dan|(talk) 16:06, 23 May 2009 (UTC)
replies: text:  Actually PDBWiki has an article all about the "PDB code" http://pdbwiki.org/index.php/PDB_code --Dan|(talk) 16:08, 23 May 2009 (UTC)
thread_title:  Need expansion/section for PDB Identifier 

message: The physical location deserves to be mentioned or listed as a coordinates. I may be mistaken, but I think the sole location for the repository is at Rutgers University (http://www.biomaps.rutgers.edu/index.php?option=com_content&task=section&id=1&Itemid=2  third paragraph). I've seen a wing of a  building at Rutgers marked Protein Data Bank: (40.524497°, -74.461634°). Pulu (talk) 18:37, 15 July 2009 (UTC)
thread_title:  Physical Location 

message: The growth trend has a link towards the official PDB site.
However had, this starts in 1976; the plot however starts in 1972. From 1972 to 1976, it would thus have 0 entries. This does not seem to make a lot of sense to me?
If SEARCH was the original database, I have another source that states that PDB started with 7 entries. Could perhaps additional verification be provided to explain why it starts at 1976, and which entries were the first one? 80.110.81.222 (talk) 21:06, 30 May 2015 (UTC)
thread_title:  Growth trend 

message: Substituted at 03:28, 30 April 2016 (UTC)
thread_title: Assessment comment

message: "100 registered structures milestone in 1982, the 1,000 in 1993, the 10,000 in 1999, and the 100,000 in 2014" 
What? 100, 1, 10 and then 100 again? Is this correct? Or is it somebody who do not know the ISO-Standard of thousand separators who has been writing this?  — Preceding unsigned comment added by 78.67.250.137 (talk) 19:34, 21 June 2017 (UTC)
thread_title:  A lot, then less, then the same again?