著者

Nobuaki Yasuo Keisuke Watanabe Hideto Hara Kentaro Rikimaru Masakazu Sekijima

出版者

Information Processing Society of Japan

雑誌

IPSJ Transactions on Bioinformatics (ISSN:18826679)

巻号頁・発行日

vol.11, pp.41-47, 2018 (Released:2018-12-10)

参考文献数

36

被引用文献数

5

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Lead optimization is an essential step in drug discovery in which the chemical structures of compounds are modified to improve characteristics such as binding affinity, target selectivity, physicochemical properties, and toxicity. We present a concept for a computational compound optimization system that outputs optimized compounds from hit compounds by using previous lead optimization data from a pharmaceutical company. In this study, to predict the drug-likeness of compounds in the evaluation function of this system, we evaluated and compared the ability to correctly predict lead optimization strategies through learning to rank methods.

著者

Nobuaki Yasuo Masakazu Sekijima

出版者

一般社団法人 情報処理学会

雑誌

IPSJ Transactions on Bioinformatics (ISSN:18826679)

巻号頁・発行日

vol.8, pp.9-13, 2015 (Released:2015-07-08)

参考文献数

25

被引用文献数

1

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We developed a new application to quantitatively evaluate the sequence conservation of ligand-binding sites by integrating information pertaining to protein structures, ligand-binding sites, and amino acid sequences. These data are visualized onto protein structures via a Jmol or PyMOL interface. The visualization is very important for structure-based drug design (SBDD). Key features of this application are the visualization of slight differences in specific ligand-binding sites and ConservationScore comparable among ligand-binding sites. Furthermore, we conducted an experiment to visualize the calculation and comparison of the ConservationScore of four viral proteins as well as an experiment to visualize the differences between proteins belonging to the human β adrenergic receptor family. This application is available at http://www.bio.gsic.titech.ac.jp/visco.html.