Molecular Framework Analysis of the Generated Database GDB-13s.

Buehler, Ye; Reymond, Jean-Louis (2023). Molecular Framework Analysis of the Generated Database GDB-13s. Journal of chemical information and modeling, 63(2), pp. 484-492. American Chemical Society 10.1021/acs.jcim.2c01107

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The generated databases (GDBs) list billions of possible molecules from systematic enumeration following simple rules of chemical stability and synthetic feasibility. To assess the originality of GDB molecules, we compared their Bemis and Murcko molecular frameworks (MFs) with those in public databases. MFs result from molecules by converting all atoms to carbons, all bonds to single bonds, and removing terminal atoms iteratively until none remain. We compared GDB-13s (99,394,177 molecules up to 13 atoms containing simplified functional groups, 22,130 MFs) with ZINC (885,905,524 screening compounds, 1,016,597 MFs), PubChem50 (100,852,694 molecules up to 50 atoms, 1,530,189 MFs), and COCONUT (401,624 natural products, 42,734 MFs). While MFs in public databases mostly contained linker bonds and six-membered rings, GDB-13s MFs had diverse ring sizes and ring systems without linker bonds. Most GDB-13s MFs were exclusive to this database, and many were relatively simple, representing attractive targets for synthetic chemistry aiming at innovative molecules.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

Buehler, Ye, Reymond, Jean-Louis

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry

ISSN:

1549-9596

Publisher:

American Chemical Society

Language:

English

Submitter:

Pubmed Import

Date Deposited:

20 Dec 2022 09:10

Last Modified:

24 Jan 2023 00:15

Publisher DOI:

10.1021/acs.jcim.2c01107

PubMed ID:

36533982

BORIS DOI:

10.48350/176144

URI:

https://boris.unibe.ch/id/eprint/176144

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