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MQN-browsers

About

We have developed a rapid nearest neighbor search tool using or recently published MQN method. This web-service may be used free of charge. For the search results the disclaimer of GDB-13 applies (see below). We gratefully acknowledge ChemAxon for donation of their license.

How to cite

To cite any application in relation to this search tools and/or the original publications, please use the appropriate reference(s):

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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:
To cite GDB-13, please reference:
To cite GDB-17, please reference:

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.

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.

I accept the Terms and Conditions.

Set Link Size

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

Entire GDB-13 (including all C/N/O/Cl/S molecules) gdb13.tgz 2.6GB

The sum of all the subsets below correspond to the entire GDB-13 above:
Graph subset (saturated hydrocarbons) gdb13.g.tgz 1.1MB
Skeleton subset (unsaturated hydrocarbons) gdb13.sk.tgz 14MB
Only carbon & nitrogen containing molecules gdb13.cn.tgz 443MB
Only carbon & oxygen containing molecules gdb13.co.tgz 299MB
Only carbon & nitrogen & oxygen containing molecules gdb13.cno.tgz 1.8G
Chlorine & sulphur containing molecules gdb13.cls.tgz 189MB

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 2.4G
GDB-13 Subset ABC(~441 Millions) ABC.smi.gz 1.7G
GDB-13 Subset ABCD(~277 Millions) ABCD.smi.gz 1.1G
GDB-13 Subset ABCDE(~140 Millions) ABCDE.smi.gz 565M
GDB-13 Subset ABCDEF(~43 Millions) ABCDEF.smi.gz 171M
GDB-13 Subset ABCDEFG(~13 Millions) ABCDEFG.smi.gz 50M
GDB-13 Subset ABCDEFGH(~1.4 Millions) ABCDEFGH.smi.gz 6.2M

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

Entire GDB-11 (including all C/N/O/F molecules) gdb11.tgz 122MB

Fragrance Like Subsets: For details please refer to Ruddigkeit et al. Journal of Cheminformatics 2014, 6:27.
FragranceDB (SuperScent + Flavornet) FragranceDB.smi 56k
TasteDB (SuperSweet + BitterDB) TasteDB.smi 44k
FragranceDB.FL (Fragrance-like subset of FragranceDB) FragranceDB.FL.smi 32k
ChEMBL.FL (Fragrance-like subset of ChEMBL) ChEMBL.FL.smi 452K
PubChem.FL Fragrance-like subset of PubChem PubChem.FL.smi 20M
ZINC.FL (Fragrance-like subset of ZINC) ZINC.FL.smi 1.3M
GDB-13.FL (Fragrance-like subset of GDB-13) GDB-13.FL.smi.gz 165M




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).

How to cite

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

Download

You can download TAGSFREE here.















clic) and amino acid type (natural or non-natural, including beta-amino acids).

How to cite

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

Download

You can download TAGSFREE here.















B>2007, 48, 4453-4455.

Download

You can download TAGSFREE here.