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Visualization of Topological Pharmacophore Space with Graph Edit Distance
http://hdl.handle.net/10061/0002000464
http://hdl.handle.net/10061/00020004648eb9aa36-402f-45d2-bd45-2b546033b87d
| アイテムタイプ | 学術雑誌論文 / Journal Article(1) | |||||||
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| 公開日 | 2024-06-13 | |||||||
| タイトル | ||||||||
| タイトル | Visualization of Topological Pharmacophore Space with Graph Edit Distance | |||||||
| 言語 | ||||||||
| 言語 | eng | |||||||
| 資源タイプ | ||||||||
| 資源タイプ | journal article | |||||||
| アクセス権 | ||||||||
| アクセス権 | open access | |||||||
| 著者 |
Nakano, Hiroshi
× Nakano, Hiroshi
× 宮尾, 知幸 |
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| 抄録 | ||||||||
| 内容記述タイプ | Abstract | |||||||
| 内容記述 | A topological pharmacophore (TP) is a chemical graph-based pharmacophore representation, where nodes are pharmacophoric features (PF) and edges are topological distances between PFs. Previously proposed sparse pharmacophore graphs (SPhGs) for TPs were shown to be effective in identifying structurally different active compounds while maintaining the interpretability of the graphs. However, one limitation of using SPhGs as queries is that many structurally similar SPhGs can be identified from a set of active compounds, requiring the classification and visualization of SPhGs, followed by an understanding of the pharmacophore hypotheses. In this study, we propose a scheme for SPhG analysis based on dimensionality reduction techniques with the graph edit distance (GED) metric. This metric enables measuring similarities among SPhGs in a quantitative manner. The visualization of SPhGs, which themselves are the graphs shared by active compounds, can help us understand the pharmacophore hypotheses as well as the data set. As a proof-of-concept study, we generated two-dimensional SPhG-maps using three dimensionality reduction techniques for six biological targets. A comparison with other pharmacophore representations was also conducted. We demonstrated knowledge extraction (interpretation of the data set) from the generated maps. Our findings include a suitable mapping algorithm as well as a pharmacophore hypothesis analysis procedure using an SPhG-map. | |||||||
| 書誌情報 |
en : ACS Omega 巻 7, 号 16, p. 14057, ページ数 14068, 発行日 2022-04-12 |
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| 出版者 | ||||||||
| 出版者 | American Chemical Society | |||||||
| ISSN | ||||||||
| 収録物識別子タイプ | EISSN | |||||||
| 収録物識別子 | 2470-1343 | |||||||
| 出版者版DOI | ||||||||
| 関連タイプ | isReplacedBy | |||||||
| 識別子タイプ | DOI | |||||||
| 関連識別子 | https://doi.org/10.1021/acsomega.2c00173 | |||||||
| 出版者版URI | ||||||||
| 関連タイプ | isReplacedBy | |||||||
| 識別子タイプ | URI | |||||||
| 関連識別子 | https://pubs.acs.org/doi/10.1021/acsomega.2c00173 | |||||||
| 権利 | ||||||||
| 権利情報Resource | https://creativecommons.org/licenses/by-nc-nd/4.0/ | |||||||
| 権利情報 | $00A9 2022 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY-NC-ND 4.0. | |||||||
| 著者版フラグ | ||||||||
| 出版タイプ | NA | |||||||
