Comments on: PubMed’s “Reported Structures” Feature http://rosettadesigngroup.com/blog/362/pubmed-reported-structures-feature/ Trading tips and news on modeling proteins, DNA, RNA, small molecules, folding, docking, design..... Sat, 28 Jan 2012 16:25:00 +0000 hourly 1 http://wordpress.org/?v=3.0 By: SM L http://rosettadesigngroup.com/blog/362/pubmed-reported-structures-feature/comment-page-1/#comment-5901 SM L Thu, 18 Jun 2009 02:04:03 +0000 http://rosettadesigngroup.com/blog/?p=362#comment-5901 Also just out on latest PDB News (16 June), <a href="http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090616" rel="nofollow">"How does a HPUB structure get released"</a>. FYI only. The email address listed there is deposit@wwpdb.org . Also just out on latest PDB News (16 June), “How does a HPUB structure get released”. FYI only. The email address listed there is deposit@wwpdb.org .

]]> By: SM L http://rosettadesigngroup.com/blog/362/pubmed-reported-structures-feature/comment-page-1/#comment-4031 SM L Sun, 26 Apr 2009 03:44:28 +0000 http://rosettadesigngroup.com/blog/?p=362#comment-4031 With regard to the PDB taking a while to catch up on publications, I've written to them before at deposit@deposit.rcsb.org to inform them that the structure I'm interested in has been published. They released it quickly after that. Just need to inform them. With regard to the PDB taking a while to catch up on publications, I’ve written to them before at deposit@deposit.rcsb.org to inform them that the structure I’m interested in has been published. They released it quickly after that. Just need to inform them.

]]> By: David Hall http://rosettadesigngroup.com/blog/362/pubmed-reported-structures-feature/comment-page-1/#comment-4017 David Hall Sat, 25 Apr 2009 19:17:08 +0000 http://rosettadesigngroup.com/blog/?p=362#comment-4017 While very nice, it seems to be connected to the PDB's data on papers related to structures, which I have found not to always be that reliable. I frequently come across papers where there's a typo in the paper title at the PDB, so they say "To be Published", but the paper is 3 years old. Also, the PDB takes a while to catch up on publications. For instance, PMID 19194458 was published last week in Nature, but there's no structure shown on Pubmed because 3ebj is still listed as "To be Published" by the PDB. This case might in fact be a case of the slight typoes because the PDB does not have parentheses around the N of PA(N) while Pubmed does, so they fail to connect. That said, the data is better than that provided by Nature, who list all PDB ids discussed in the paper, not separating out what the actual new crystal is. For instance, in that paper, they pretend it also deposited 2ixs and 1wdj (http://www.nature.com/nature/journal/v458/n7240/pdb/nature07720_PDB1.html). Nature's attempt at extracting the information is a complete mess. While very nice, it seems to be connected to the PDB’s data on papers related to structures, which I have found not to always be that reliable. I frequently come across papers where there’s a typo in the paper title at the PDB, so they say “To be Published”, but the paper is 3 years old. Also, the PDB takes a while to catch up on publications. For instance, PMID 19194458 was published last week in Nature, but there’s no structure shown on Pubmed because 3ebj is still listed as “To be Published” by the PDB. This case might in fact be a case of the slight typoes because the PDB does not have parentheses around the N of PA(N) while Pubmed does, so they fail to connect.

That said, the data is better than that provided by Nature, who list all PDB ids discussed in the paper, not separating out what the actual new crystal is. For instance, in that paper, they pretend it also deposited 2ixs and 1wdj (http://www.nature.com/nature/journal/v458/n7240/pdb/nature07720_PDB1.html). Nature’s attempt at extracting the information is a complete mess.

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