Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces

Awale, Mahendra; Reymond, Jean-Louis (2015). Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces. Journal of chemical information and modeling, 55(8), pp. 1509-1516. American Chemical Society 10.1021/acs.jcim.5b00182

[img] Text
acs%2Ejcim%2E5b00182.pdf - Published Version
Restricted to registered users only
Available under License Publisher holds Copyright.

Download (589kB) | Request a copy

An Internet portal accessible at www.gdb.unibe.ch has been set up to automatically generate color-coded similarity maps of the ChEMBL database in relation to up to two sets of active compounds taken from the enhanced Directory of Useful Decoys (eDUD), a random set of molecules, or up to two sets of user-defined reference molecules. These maps visualize the relationships between the selected compounds and ChEMBL in six different high dimensional chemical spaces, namely MQN (42-D molecular quantum numbers), SMIfp (34-D SMILES fingerprint), APfp (20-D shape fingerprint), Xfp (55-D pharmacophore fingerprint), Sfp (1024-bit substructure fingerprint), and ECfp4 (1024-bit extended connectivity fingerprint). The maps are supplied in form of Java based desktop applications called “similarity mapplets” allowing interactive content browsing and linked to a “Multifingerprint Browser for ChEMBL” (also accessible directly at www.gdb.unibe.ch) to perform nearest neighbor searches. One can obtain six similarity mapplets of ChEMBL relative to random reference compounds, 606 similarity mapplets relative to single eDUD active sets, 30 300 similarity mapplets relative to pairs of eDUD active sets, and any number of similarity mapplets relative to user-defined reference sets to help visualize the structural diversity of compound series in drug optimization projects and their relationship to other known bioactive compounds.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Other Institutions > NCCR TransCure
08 Faculty of Science > Departement of Chemistry and Biochemistry

UniBE Contributor:

Awale, Mahendra and Reymond, Jean-Louis

Subjects:

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

ISSN:

1549-9596

Publisher:

American Chemical Society

Language:

English

Submitter:

Sandra Tanja Zbinden Di Biase

Date Deposited:

22 Jan 2016 14:54

Last Modified:

06 Sep 2016 12:35

Publisher DOI:

10.1021/acs.jcim.5b00182

PubMed ID:

26207526

BORIS DOI:

10.7892/boris.74718

URI:

https://boris.unibe.ch/id/eprint/74718

Actions (login required)

Edit item Edit item
Provide Feedback