Reymond Research Group

University of Bern


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.

An artistic representation of the chemical universe
Figure 2. An artistic representation of the chemical universe. Molecules emerge in series from an ocean of possibilities through selection of proper atomic combinations. (Tobias Fink, Ph.D. thesis, 2006).

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

The GDB databases are hosted on the public University of Berne FTP-Server. You can download the databases and subsets of it using the links below. 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). To see the structures in drawing format, we suggest MarvinView, a free chemical structure viewer from ChemAxon.

Set Link Size
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
Other
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
Scaffold Hopping: There is a diversity driven fragment library (extracted from GDB-17) available that has been indexed for ReCore from BioSolveIT.
3D Scaffold Hopping tool ReCore 165 MB

Tagsfree Encoding System for Combinatorial Peptide Libraries

About

TAGSFREE is a program for designing split-and-mix peptide libraries that can be decoded by amino acid analysis. The analysis is independent of peptide topology (linear, branched, cyclic) and amino acid type (natural or non-natural, including beta-amino acids).

Peptides on beads
Figure 3. Generation on of a combinatorial peptide library using beads.

How to cite

Any work based on the TAGSFREE method must cite the following publications:

A General Method for Designing Combinatorial Peptide Libraries Decodable by Amino Acid Analysis. Kofoed J.; Reymond J.-L. J. Comb. Chem. 2007, 9, 1046-1052.

Identification of protease substrates by combinatorial profiling on tentagel beads. Kofoed J.; Reymond J.-L. Chem. Commun. 2007, 48, 4453-4455.

Download

You can download TAGSFREE here.