Design of chemical space networks incorporating compound distance relationships [version 1; referees: 2 approved]
Networks, in which nodes represent compounds and edges pairwise similarity relationships, are used as coordinate-free representations of chemical space. So-called chemical space networks (CSNs) provide intuitive access to structural relationships within compound data sets and can be annotated with a...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
F1000 Research Ltd
2016-11-01
|
| Series: | F1000Research |
| Subjects: | |
| Online Access: | https://f1000research.com/articles/5-2634/v1 |
| _version_ | 1818328879233761280 |
|---|---|
| author | Antonio de la Vega de León Jürgen Bajorath |
| author_facet | Antonio de la Vega de León Jürgen Bajorath |
| author_sort | Antonio de la Vega de León |
| collection | DOAJ |
| description | Networks, in which nodes represent compounds and edges pairwise similarity relationships, are used as coordinate-free representations of chemical space. So-called chemical space networks (CSNs) provide intuitive access to structural relationships within compound data sets and can be annotated with activity information. However, in such similarity-based networks, distances between compounds are typically determined for layout purposes and clarity and have no chemical meaning. By contrast, inter-compound distances as a measure of dissimilarity can be directly obtained from coordinate-based representations of chemical space. Herein, we introduce a CSN variant that incorporates compound distance relationships and thus further increases the information content of compound networks. The design was facilitated by adapting the Kamada-Kawai algorithm. Kamada-Kawai networks are the first CSNs that are based on numerical similarity measures, but do not depend on chosen similarity threshold values. |
| first_indexed | 2024-12-13T12:39:10Z |
| format | Article |
| id | doaj.art-c40e2124416c427e825a5be13bab45a2 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-13T12:39:10Z |
| publishDate | 2016-11-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-c40e2124416c427e825a5be13bab45a22022-12-21T23:45:42ZengF1000 Research LtdF1000Research2046-14022016-11-01510.12688/f1000research.10021.110797Design of chemical space networks incorporating compound distance relationships [version 1; referees: 2 approved]Antonio de la Vega de León0Jürgen Bajorath1Department of Life Science Informatics, Rheinische Friedrich-Wilhelms-Universität, Bonn, GermanyDepartment of Life Science Informatics, Rheinische Friedrich-Wilhelms-Universität, Bonn, GermanyNetworks, in which nodes represent compounds and edges pairwise similarity relationships, are used as coordinate-free representations of chemical space. So-called chemical space networks (CSNs) provide intuitive access to structural relationships within compound data sets and can be annotated with activity information. However, in such similarity-based networks, distances between compounds are typically determined for layout purposes and clarity and have no chemical meaning. By contrast, inter-compound distances as a measure of dissimilarity can be directly obtained from coordinate-based representations of chemical space. Herein, we introduce a CSN variant that incorporates compound distance relationships and thus further increases the information content of compound networks. The design was facilitated by adapting the Kamada-Kawai algorithm. Kamada-Kawai networks are the first CSNs that are based on numerical similarity measures, but do not depend on chosen similarity threshold values.https://f1000research.com/articles/5-2634/v1Bioinformatics |
| spellingShingle | Antonio de la Vega de León Jürgen Bajorath Design of chemical space networks incorporating compound distance relationships [version 1; referees: 2 approved] F1000Research Bioinformatics |
| title | Design of chemical space networks incorporating compound distance relationships [version 1; referees: 2 approved] |
| title_full | Design of chemical space networks incorporating compound distance relationships [version 1; referees: 2 approved] |
| title_fullStr | Design of chemical space networks incorporating compound distance relationships [version 1; referees: 2 approved] |
| title_full_unstemmed | Design of chemical space networks incorporating compound distance relationships [version 1; referees: 2 approved] |
| title_short | Design of chemical space networks incorporating compound distance relationships [version 1; referees: 2 approved] |
| title_sort | design of chemical space networks incorporating compound distance relationships version 1 referees 2 approved |
| topic | Bioinformatics |
| url | https://f1000research.com/articles/5-2634/v1 |
| work_keys_str_mv | AT antoniodelavegadeleon designofchemicalspacenetworksincorporatingcompounddistancerelationshipsversion1referees2approved AT jurgenbajorath designofchemicalspacenetworksincorporatingcompounddistancerelationshipsversion1referees2approved |