著者

Yuki Sugawara Masaaki Kotera Kenichi Tanaka Kimito Funatsu

出版者

Division of Chemical Information and Computer Sciences The Chemical Society of Japan

雑誌

Journal of Computer Aided Chemistry (ISSN:13458647)

巻号頁・発行日

vol.20, pp.7-17, 2019 (Released:2019-06-11)

参考文献数

27

被引用文献数

4

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Fluorescent substances are used in a wide range of applications, and the method that effectively design molecules having desirable absorption and emission wavelength is required. In this study, we used boron-dipyrromethene (BODIPY) compounds as a case study, and constructed high precision wavelength prediction model using ensemble learning. Prediction accuracy improved in stacking model using RDKit descriptors and Morgan fingerprint. The variables related to the molecular skeleton and the conjugation length were shown to be important. We also proposed an applicability domain (AD) estimation model that directly use the descriptors based on Tanimoto distance. The performance of the AD models was shown better than the OCSVM-based model. Using our proposed stacking model and AD model, newly generated compounds were screened and we obtained 602 compounds which were estimated inside the AD in both absorption wavelength and emission wavelength.

著者

Masaaki Kotera Susumu Goto

出版者

一般社団法人 日本生物物理学会

雑誌

Biophysics and Physicobiology (ISSN:21894779)

巻号頁・発行日

vol.13, pp.195-205, 2016 (Released:2016-07-15)

参考文献数

86

被引用文献数

15

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Metabolic pathway reconstruction presents a challenge for understanding metabolic pathways in organisms of interest. Different strategies, i.e., reference-based vs. de novo, must be used for pathway reconstruction depending on the availability of well-characterized enzymatic reactions. If at least one enzyme is already known to catalyze a reaction, its amino acid sequence can be used as a reference for identifying homologous enzymes in the genome of an organism of interest. Where there is no known enzyme able to catalyze a corresponding reaction, however, the reaction and the corresponding enzyme must be predicted de novo from chemical transformations of the putative substrate-product pair. This review summarizes studies involving reference-based and de novo metabolic pathway reconstruction and discusses the importance of the classification and structure-function relationships of enzymes.