Reymond Research Group

University of Bern

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Download Form - GDBs

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 1. 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.


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 2. 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.


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