Open AccessExploring the Chemical Space of Known and Unknown Organic Small Molecules at www.gdb.unibe.ch
Author(s) -
JeanLouis Reymond,
Lorenz C. Blum,
Ruud van Deursen
Publication year - 2011
Publication title -
chimia
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.387
H-Index - 55
eISSN - 2673-2424
pISSN - 0009-4293
DOI - 10.2533/chimia.2011.863
Subject(s) - chemical space , pubchem , cheminformatics , molecule , organic molecules , space (punctuation) , chemical database , chemistry , simple (philosophy) , universe , database , computer science , physics , computational chemistry , drug discovery , organic chemistry , astrophysics , biochemistry , philosophy , epistemology , operating system
Organic small molecules are of particular interest for medicinal chemistry since they comprise many biologically active compounds which are potential drugs. To understand this vast chemical space, we are enumerating all possible organic molecules to create the chemical universe database GDB, which currently comprises 977 million molecules up to 13 atoms of C, N, O, Cl and S. Furthermore, we have established a simple classification method for organic molecules in form of the MQN (molecular quantum numbers) system, which is an equivalent of the periodic system of the elements. Despite its simplicity the 42 dimensional MQN system is surprisingly relevant with respect to bioactivity, as evidenced by the fact that groups of biosimilar compounds form close groups in MQN space. The MQN space of the known organic molecules in PubChem and of the unknown molecules in the Chemical Universe Database GDB-13 can be searched interactively using browser tools freely accessible at www.gdb.unibe.ch.