Table 1.
List of current benchmarking data sets, made available from years of 2000 to 2014. The source of ligands, decoys, ratio of decoys per ligand and public access address are included.
| Publication Year |
Name | Author(s) | Source of ligands | Source of decoys | Ratio of decoys per ligand |
Public access (accessed in Jun. 2014) | |
|---|---|---|---|---|---|---|---|
| SBVS | 2000–11 | Rognan’s decoy set | Rognan | literature | Advanced Chemical Directory (ACD) | undefined | http://bioinfo-pharma.u-strasbg.fr/labwebsite/download.html |
| 2002–09 | Shoichet's decoy set | Shoichet | literature | MDL Drug Data Report (MDDR) ver2000.2 |
undefined | ||
| 2003–06 | Diller's decoy set | Diller | literature | MDL Drug Data Report (MDDR) | undefined | ||
| 2005–06 | Jain's decoy set | Jain | PDBbind database | ZINC "drug-like" subset | undefined | http://www.jainlab.org/downloads.html | |
| 2006–10 | Directory of Useful Decoys (DUD) |
Irwin & Shoichet | literature, PDBbind, etc. | ZINC "drug-like" subset | 36 | http://dud.docking.org/ | |
| 2007 | Directory of Useful Decoys (DUD) Clusters |
Good & Oprea | DUD ligands | DUD decoys | undefined | http://dud.docking.org/ | |
| 2007 | WOMBAT datasets | Good & Oprea | WOMBAT | DUD decoys | undefined | http://dud.docking.org/ | |
| 2010 | Charge Matched DUD | Shoichet | DUD | ZINC database | 36 | http://dud.docking.org/ | |
| 2011–01 | Virtual Decoy Sets (VDS) | Wallach and Lilien | DUD | virtual molecules | 36 | http://compbio.cs.toronto.edu/VDS | |
| 2011–07 | Demanding Evaluation Kits for Objective in Silico Screening (DEKOIS) |
Boeckler | BindingDB | ZINC database (version 8, November 2009) |
30 | http://www.dekois.com/dekois_orig.html | |
| 2011–12 | G protein-coupled receptor (GPCR) Ligand Library (GLL) / Decoy Database (GDD) |
Cavasotto | GLIDA | ZINC database (accessed in Jan. 2011) | 39 | http://cavasotto-lab.net/Databases/GDD/Download/ | |
| 2012-01 | DecoyFinder | Cereto-Massague & Garcia-Vallve |
user-supplied | ZINC database or others | any (user- defined) |
http://urvnutrigenomica-ctns.github.io/DecoyFinder/ | |
| 2012-06 | Directory of Useful Decoys Enhanced (DUD-E) |
Irwin & Shoichet | ChEMBL | ZINC | 50 | http://dude.docking.org/ | |
| 2013-05 | DEKOIS 2.0 | Boeckler | BindingDB | ZINC | 30 | http://www.dekois.com/ | |
| 2014-01 | Nuclear Receptors ligands and structures benchmarking database (NRLiSt BDB) |
Matthieu Montes | ChEMBL database or the Pubchem database |
DUD-E decoy maker & ZINC | 50 | http://nrlist.drugdesign.fr | |
| LBVS | 2009-01 | Maximum Unbiased Validation (MUV) |
Baumann | PubChem (actives with EC50) |
PubChem (inactives) | 500 | http://www.pharmchem.tu-bs.de/lehre/baumann/MUV.html |
| 2009-05 | DUD LIB V1.0 | Good and Oprea | DUD clusters | DUD decoys | undefined | http://dud.docking.org/ | |
| 2011-09 | DataBase of REProducible VIrtual Screens (REPROVIS- DB) |
Bajorath | literature (quanlifying hits) |
literature (screening database) | undefined | http://www.lifescienceinformatics.uni-bonn.de | |