Table 7.
Databases of chemicals/compounds, bioactivities and target proteins, statistics and links
| Compound and bioactivity databases | Statisticsa |
Website | Version | ||
|---|---|---|---|---|---|
| Compounds | Targets | Interactions | |||
| PubChem [1] | 93 977 773 (C) 235 653 627 (S) | 10 341 (P) | 233 799 255 (I) 1 252 820 (E) | https://pubchem.ncbi.nlm.nih.gov | 03.12.2017 |
| ChEMBL [2] | 1 735 442 (C) | 11 538 (P) | 14 675 320 (I) 1 302 147 (E) | https://www.ebi.ac.uk/chembl | v23 |
| DrugBank [5] | 9591 (D) | 4270 (P) | 16 748 (I) | http://www.drugbank.ca | v5.0 |
| STITCH [167] | ∼500 000 (C) | 9 643 763 (P) | ∼1.6 billion (I) | http://stitch-beta.embl.de | v5.0 |
| BindingDB [168] | 635 301 (C) | 7000 (P) | 1 419 347 (I) | http://www.bindingdb.org | 03.12.2017 |
| BindingMoad [169] | 12 440 (C) | 7599 (F) | 25769 (I) | http://bindingmoad.org | Rel. 2014 |
| KEGG [170] | 18 211 (C) 10 484 (D) | 976 (P) | 6502 (I) | http://www.kegg.jp | Rel. 84.1 |
| DCDB [171] | 904 (D) 1363 (DC) | 805 (P) | – | http://www.cls.zju.edu.cn/dcdb/index.jsf | v2.0 |
| T3DB [172] | 3673 (T) | 2087 (P) | 42471 (I) | http://www.t3db.ca/ | v2.0 |
|
| |||||
| Side effect databases | Statisticsa | Website | Version | ||
|
| |||||
| SIDER [173] | 1430 (D), 5868 (SE), 139 756 (A) | http://sideeffects.embl.de | v4.1 | ||
|
| |||||
| Metabolome databases | Statisticsa | Website | Version | ||
|
| |||||
| HMDB [174] | 114 089 (M) | http://www.hmdb.ca/ | v4.0 | ||
|
| |||||
|
Chemical databases |
Compounds |
|
|
Website |
Version |
| ChemSpider [3] | ∼62 000 000 (C) | http://www.chemspider.com | 03.12.2017 | ||
| ChEBI [4] | 53 495 (C) | https://www.ebi.ac.uk/chebi | Rel. 158 | ||
| ZINC [175] | ∼100 000 000 (C) | http://zinc15.docking.org/ | ZINC 15 | ||
|
| |||||
| Target databases | Statisticsa | Website | Version | ||
|
| |||||
| AAindex [176] | AAindex1:566 indices, AAindex2:94 matrices, AAindex3:47 contact potential matrices | http://www.genome.jp/aaindex | Rel. 9.2 | ||
| UniProtKB [80] | Swiss-Prot: 556 196 (P), TrEMBL: 98 705 220 (P) | http://www.uniprot.org | v2017_11 | ||
| InterPro [177] | 2128 (SF), 20 410 (F), 8840 (DM) | https://www.ebi.ac.uk/interpro/ | v66 | ||
| Pfam [178] | 16 712 (F) | http://pfam.xfam.org/ | v31.0 | ||
| RCSB PDB [81] | 125 799 (P) | https://www.rcsb.org/ | 28.11.2017 | ||
| sc-PDB [179] | 6326 (C), 4782 (P), 16 034 (I) | http://bioinfo-pharma.u-strasbg.fr/scPDB/ | Rel. 2017 | ||
| CATH [180] | 6119 (SF), 434 857 (DM) | http://www.cathdb.info | v4.2 | ||
| SCOPe [181] | 2008 (SF), 4851 (F), 244 326 (DM) | https://scop.berkeley.edu | v2.06 | ||
a
Abbreviations in the statistic column: compound (C), substance (S), drug (D) protein (P), protein family (F), interaction (I), experiments (E), associations (A), toxin (T), side effects (SE), drug combination (DC), metabolite (M), domain (DM), superfamily (SF).