I seach the PDB statistics and it is possible to know the amount of protein structures, also the amount of RNA-protein structures. But I would like to know the amount of structures related to complexes between two proteins or an statistics involving growing of structures at PDB per year considering only protein-protein complexs.
If it is not possible to search directly at DB statistics, please let me know about any recent paper or database talking about amount of reported protein-protein complexes.
Hi,
You can refine you search in the PDB for this purpose:
1 - In the PDB go to Search menu and click in Drilldown search
2 - Select Protein Stoichiometry field. At the right you will see a pie chart with the Monomer, Homomer and Heteromer statistics in the PDB
3 - Click the one you prefer separately. Refine your query with as you wish with the pie charts. In the Protein Stoichiometry field you can select the N-mer to select dimers, trimers,etc.
4 - At the begging of the entries list you will see the Reports menu. Click it and select Customizable table.
5 - Select the fields you are interested in, ej. Deposit date. Download the data
6 - Merge the data and plot vs Deposition date
There is a database http://www.3dcomplex.org with this information, but I think it is not properly updated.
Hope this help
Best
Yasser
This is very easy to do at the Protein Data Bank in Europe. The following URL gives all entries released in the PDB in 2015:
http://www.ebi.ac.uk/pdbe/entry/search/index?release_year:2015
On the left you will see a 'facets' menu, showing how these can be broken down, under "Assembly composition" you can see that there are 239 DNA-Protein complexes, 1421 protein/protein complex (these are complexes of different proteins) and 5641 'protein structure' (monomers of homo-oligomers)
For different years, simply change the year in the URL
Thanks a lot to both of you!!!
Yasser: I saw the 3Dcomplex database but in fact it looks not updated
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