DOI: 10.5281/zenodo.7041051
title: GDB Databases

description: <strong>About</strong> GDB-11 enumerates small organic molecules up to 11 atoms of C, N, O and F following simple chemical stability and synthetic feasibility rules.<br> 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. <strong>How to cite</strong> 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. <em>Chem. Inf. Model.</em> <strong>2007</strong>, 47, 342-353. Virtual Exploration of the Small Molecule Chemical Universe below 160 Daltons. Fink, T.; Bruggesser, H.; Reymond, J.-L. <em>Angew. Chem. Int. Ed.</em> <strong>2005</strong>, 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. <em>J. Am. Chem. Soc.</em>, <strong>2009</strong>, 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. <em>J. Chem. Inf. Model.</em>, <strong>2012</strong>, 52, 2864-2875. <strong>Download </strong> 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). <br> <strong>GDB-17</strong><br> GDB-17-Set (50 million) GDB17.50000000.smi.gz 314 MB<br> Lead-like Set (100-350 MW & 1-3 clogP)(11 million) GDB17.50000000LL.smi.gz 75 MB<br> 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 <strong>GDB-13</strong><br> Entire GDB-13 (including all C/N/O/Cl/S molecules) gdb13.tgz 2.6 GB<br> GDB-13 Subsets (The sum of all the subsets below correspond to the entire GDB-13 above)<br> Graph subset (saturated hydrocarbons) gdb13.g.tgz 1.1 MB<br> Skeleton subset (unsaturated hydrocarbons) gdb13.sk.tgz 14 MB<br> Only carbon & nitrogen containing molecules gdb13.cn.tgz 443 MB<br> Only carbon & oxygen containing molecules gdb13.co.tgz 299 MB<br> Only carbon & nitrogen & oxygen containing molecules gdb13.cno.tgz 1.8 GB<br> Chlorine & sulphur containing molecules gdb13.cls.tgz 189 MB GDB-13 Subsets (For details please refer to the Table 2 in <em>J Comput Aided Mol Des</em> <strong>2011</strong> 25:637 to 647)<br> GDB-13 Subset AB (~635 Millions) AB.smi.gz 2.4 GB<br> GDB-13 Subset ABC (~441 Millions) ABC.smi.gz 1.7 GB<br> GDB-13 Subset ABCD (~277 Millions) ABCD.smi.gz 1.1 GB<br> GDB-13 Subset ABCDE (~140 Millions) ABCDE.smi.gz 565 MB<br> GDB-13 Subset ABCDEF (~43 Millions) ABCDEF.smi.gz 171 MB<br> GDB-13 Subset ABCDEFG (~13 Millions) ABCDEFG.smi.gz 50 MB<br> GDB-13 Subset ABCDEFGH (~1.4 Millions) ABCDEFGH.smi.gz 6.2 MB<br> GDB-13 Random Sample. Annotated with frequency and log-likelihood (Please refer to Exploring the GDB-13 chemical space using deep generative models)<br> GDB-13 Random Sample (1 Million) gdb13.1M.freq.ll.smi.gz 14.8 MB <strong>FDB-17</strong><br> FDB-17 FDB-17-fragmentset.smi.gz 62.2 MB <br> <strong>GDB4c</strong><br> GDB4c (SMILES) GDB4c.smi.gz 6.2 MB<br> GDB4c3D (SMILES) GDB4c3D.smi.gz 161 MB<br> GDB4c3D (SDF) GDB4c3D.sdf.tar.gz 2 GB <br> <strong>Other</strong><br> GDBMedChem (SMILES) GDBMedChem.smi 276 MB<br> GDBChEMBL (SMILES) GDBChEMBL.smi 353.6 MB<br> GDB-13 random selection (1 million) gdb13.rand1M.smi.gz 7.2 MB<br> Fragment-like subset (Rule of three) gdb13.frl.tgz 1.2 GB<br> Dark matter universe up to 9 heavy atoms dmu9.tgz 87 MB <strong>GDB-11</strong><br> Entire GDB-11 (including all C/N/O/F molecules) gdb11.tgz 122 MB<br> Fragrance Like Subsets: For details please refer to Ruddigkeit <em>et al. Journal of Cheminformatics</em> <strong>2014</strong>, 6:27<br> FragranceDB (SuperScent + Flavornet) FragranceDB.smi 56 KB<br> TasteDB (SuperSweet + BitterDB) TasteDB.smi 44 KB<br> FragranceDB.FL (Fragrance-like subset of FragranceDB) FragranceDB.FL.smi 32 KB<br> ChEMBL.FL (Fragrance-like subset of ChEMBL) ChEMBL.FL.smi 452 KB<br> PubChem.FL Fragrance-like subset of PubChem PubChem.FL.smi 20 MB<br> ZINC.FL (Fragrance-like subset of ZINC) ZINC.FL.smi 1.3 MB<br> GDB-13.FL (Fragrance-like subset of GDB-13) GDB-13.FL.smi.gz 165 MB <strong>Terms and conditions</strong>: 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.
description: {"references": ["Fink, T.; Reymond, J.-L. J. Chem. Inf. Model. 2007, 47, 342-353.", "Fink, T.; Bruggesser, H.; Reymond, J.-L. Angew. Chem. Int. Ed. 2005, 44, 1504-1508.", "Blum L. C.; Reymond J.-L. J. Am. Chem. Soc., 2009, 131, 8732-8733.", "Ruddigkeit L., van Deursen R., Blum L. C.; Reymond J.-L. J. Chem. Inf. Model., 2012, 52, 2864-2875."]}