Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds

Table 2 Compounds-per-protein and per-document.

Database or subset	Document count	Protein ID type	Total proteins	Human proteins	Cpds-per-protein	Cpds-per-document
GVKBIO	87747	Entrez Gene	3292	1468	604	22
GVKBIO journals	51810	Entrez Gene	2660	1146	239	12
GVKBIO patents	35937	Entrez Gene	1765	952	815	40
GVKBIO DD	26825	Entrez Gene	733	339	5	0.14
GVKBIO CCD	27286	Entrez Gene	1224	610	7	0.32
WOMBAT	10205	Swiss-Prot	1979	1095	91	18
DrugBank	n/a	Swiss-Prot	1625	1356	3	n/a
PubChem actives	n/a	RefSeq	72	n/a	104	n/a
PubChem PDB	n/a	RefSeq	818	n/a	14	n/a
BindingDB	1142	Swiss-Prot	297	97	112	19
MDDR	137754	n/a	n/a	n/a	n/a	1.4
DNP	7765	n/a	n/a	n/a	n/a	18

Column three is the type of protein identifier used for the count of all species (column four) and human proteins (column five). In columns six and seven the filtered compound totals are taken from Additional file 1. The compound ratios are calculated with respect to total proteins and documents. For boxes labelled n/a the information was either not applicable or not available. For reference we have included a compounds-per-protein calculation for the PubChem actives subset even though there are no document-protein links analogous to the other sources.

ISSN: 1758-2946