Thanks ! I got it ! Sandra
On Mon, Oct 15, 2012 at 7:23 PM, Das, Debanu <[email protected]>wrote: > Hi Sandra, > > Yes, there are several ways of getting this information. > > Go to PDB website Advanced Search section. In the Query Type pull down, > select All and then select "Remove Similar Sequences at 30% identity". You > will have to select 30% cut off in the pull down menu. This will result in > ~22000 structures out of ~85000 PDB entries. Fine tune the search by > searching for only proteins (and xray or NMR). > > Also note that almost all structures deposited from the various centers of > the PSI (Protein Structure Initiative) meet this criteria of novelty (many > are actually in the 5-20% seq identity range). > > From the PDB website, click on Advanced Search. From the drop down menu, > select "Structural Genomics Project" and under Centers select "All". You > will see ~11500 entries. > You can see some PSI metrics at: > http://targetdb.pdb.org/Metrics/MilestonesTables.html > > In addition, the following papers will illustrate the PSI unique > structures.: > > 1) http://www.ncbi.nlm.nih.gov/pubmed/16424331 > Science. 2006 Jan 20;311(5759):347-51. > The impact of structural genomics: expectations and outcomes. > Chandonia JM, Brenner SE. > Berkeley Structural Genomics Center, Physical Biosciences Division, > Lawrence Berkeley National Laboratory, and Department of Plant and > Microbial Biology, University of California, Berkeley, CA 94720, USA. > > > 2) http://www.ncbi.nlm.nih.gov/pubmed/19787035 > PLoS Biol. 2009 Sep;7(9):e1000205. Epub 2009 Sep 29. > Exploration of uncharted regions of the protein universe. > Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson > IA, Godzik A. > Joint Center for Structural Genomics, Bioinformatics Core, Burnham > Institute for Medical Research, La Jolla, California, United States of > America. > > 3) http://www.ncbi.nlm.nih.gov/pubmed/19523904 > Structure. 2009 Jun 10;17(6):869-81. > PSI-2: structural genomics to cover protein domain family space. > Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser > A, Godzik A, Rost B, Orengo C. > Department of Structural and Molecular Biology, University College of > London, London WC1E6BT, UK. [email protected] > > Hope this helps. > > Thanks, > Debanu. > ________________________________________ > From: CCP4 bulletin board [[email protected]] On Behalf Of Sandra > Quarantini [[email protected]] > Sent: Monday, October 15, 2012 3:53 AM > To: [email protected] > Subject: [ccp4bb] unique structures > > HI! Does anybody know the number or a likely number of unique structures > (solved by Xray) deposited in PDB every year???? (Unique structures I mean > less than 30% identical in sequence to proteins for which structures had > already been determined) > I could not find this data ın PDB . Is eventually possible to get an > estimate of this number by calculating the number of structures solved by > MAD/SAD ...? thank you!! > -- Dr Sandra Quarantini Department of Biomedical Sciences University of Padua Viale G. Colombo 3 35131 Padova - ITALY Voice: +393494792030 Email: [email protected] http://it.linkedin.com/pub/sandra-quarantini/30/b74/88
