GDB Databases

About

GDB-11 enumerates small organic molecules up to 11 atoms of C, N, O and F following simple chemical stability and synthetic feasibility rules.
GDB-13 enumerates small organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules. With 977 468 314 structures, GDB-13 is the largest publicly available small organic molecule database to date.

How to cite

To cite GDB-11, please reference:

Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physico-chemical properties, compound classes and drug discovery. Fink, T.; Reymond, J.-L. J. Chem. Inf. Model. 2007, 47, 342-353.

Virtual Exploration of the Small Molecule Chemical Universe below 160 Daltons. Fink, T.; Bruggesser, H.; Reymond, J.-L. Angew. Chem. Int. Ed. 2005, 44, 1504-1508.

To cite GDB-13, please reference:

970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13. Blum L. C.; Reymond J.-L. J. Am. Chem. Soc., 2009, 131, 8732-8733.

To cite GDB-17, please reference:

Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17. Ruddigkeit Lars, van Deursen Ruud, Blum L. C.; Reymond J.-L. J. Chem. Inf. Model., 2012, 52, 2864-2875.

Download

You can download the databases and subsets of it using the links provided. All the molecules are stored in dearomatized, canonized SMILES format and compressed as tar/gz archive (for Windows users: Download 7-zip to open archives).

GDB-17
GDB-17-Set (50 million)     GDB17.50000000.smi.gz     314 MB
Lead-like Set (100-350 MW & 1-3 clogP)(11 million)     GDB17.50000000LL.smi.gz     75 MB
Lead-like Set (100-350 MW & 1-3 clogP) without small rings (3-4 ring atoms)(0.8 million)   GDB17.50000000LLnoSR.smi.gz     55 MB

GDB-13
Entire GDB-13 (including all C/N/O/Cl/S molecules)     gdb13.tgz     2.6 GB
GDB-13 Subsets (The sum of all the subsets below correspond to the entire GDB-13 above)
Graph subset (saturated hydrocarbons)     gdb13.g.tgz     1.1 MB
Skeleton subset (unsaturated hydrocarbons)     gdb13.sk.tgz     14 MB
Only carbon & nitrogen containing molecules     gdb13.cn.tgz     443 MB
Only carbon & oxygen containing molecules     gdb13.co.tgz     299 MB
Only carbon & nitrogen & oxygen containing molecules     gdb13.cno.tgz     1.8 GB
Chlorine & sulphur containing molecules     gdb13.cls.tgz     189 MB

GDB-13 Subsets (For details please refer to the Table 2 in J Comput Aided Mol Des 2011 25:637 to 647)
GDB-13 Subset AB (~635 Millions)     AB.smi.gz     2.4 GB
GDB-13 Subset ABC (~441 Millions)     ABC.smi.gz     1.7 GB
GDB-13 Subset ABCD (~277 Millions)     ABCD.smi.gz     1.1 GB
GDB-13 Subset ABCDE (~140 Millions)     ABCDE.smi.gz     565 MB
GDB-13 Subset ABCDEF (~43 Millions)     ABCDEF.smi.gz     171 MB
GDB-13 Subset ABCDEFG (~13 Millions)     ABCDEFG.smi.gz     50 MB
GDB-13 Subset ABCDEFGH (~1.4 Millions)     ABCDEFGH.smi.gz     6.2 MB
GDB-13 Random Sample. Annotated with frequency and log-likelihood (Please refer to Exploring the GDB-13 chemical space using deep generative models)
GDB-13 Random Sample (1 Million)     gdb13.1M.freq.ll.smi.gz     14.8 MB

FDB-17
FDB-17     FDB-17-fragmentset.smi.gz     62.2 MB

GDB4c
GDB4c (SMILES)     GDB4c.smi.gz     6.2 MB
GDB4c3D (SMILES)     GDB4c3D.smi.gz     161 MB
GDB4c3D (SDF)     GDB4c3D.sdf.tar.gz     2 GB

Other
GDBMedChem (SMILES)     GDBMedChem.smi     276 MB
GDBChEMBL (SMILES)     GDBChEMBL.smi     353.6 MB
GDB-13 random selection (1 million)     gdb13.rand1M.smi.gz     7.2 MB
Fragment-like subset (Rule of three)     gdb13.frl.tgz     1.2 GB
Dark matter universe up to 9 heavy atoms     dmu9.tgz     87 MB

GDB-11
Entire GDB-11 (including all C/N/O/F molecules)     gdb11.tgz     122 MB
Fragrance Like Subsets: For details please refer to Ruddigkeit et al. Journal of Cheminformatics 2014, 6:27
FragranceDB (SuperScent + Flavornet)     FragranceDB.smi     56 KB
TasteDB (SuperSweet + BitterDB)     TasteDB.smi     44 KB
FragranceDB.FL (Fragrance-like subset of FragranceDB)     FragranceDB.FL.smi     32 KB
ChEMBL.FL (Fragrance-like subset of ChEMBL)     ChEMBL.FL.smi     452 KB
PubChem.FL Fragrance-like subset of PubChem     PubChem.FL.smi     20 MB
ZINC.FL (Fragrance-like subset of ZINC)     ZINC.FL.smi     1.3 MB
GDB-13.FL (Fragrance-like subset of GDB-13)     GDB-13.FL.smi.gz     165 MB

Terms and conditions: The GDB databases may be downloaded free of charge. In published research involving GDB, cite the appropriate references mentioned above. GDB must not be used as part of or in patents. GDB and large portions thereof must not be redistributed without the express written permission of Jean-Louis Reymond.