CONFERENCES
2015
2.
Moonshik Shin; Sungyoung Yoo; Suhyun Ha; Kyungrin Noh; Doheon Lee
Abstract | Links | BibTeX | Dimensions | Tags: ADME, Bioinformatics, Natural product
@conference{shin2015identifying,
title = {Identifying Potential Bioactive Compounds of Natural Products by Combining ADMET Prediction Methods},
author = {Moonshik Shin and Sungyoung Yoo and Suhyun Ha and Kyungrin Noh and Doheon Lee},
url = {https://dl.acm.org/doi/abs/10.1145/2811163.2811168},
doi = {10.1145/2811163.2811168},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
booktitle = {Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics},
pages = {19–19},
publisher = {CIKM},
abstract = {Herbs consist of various chemical compounds. Thus, identifying potential bioactive compounds from those diversity is an important task for studies in the herb, food and natural products. Even though various computational approaches are developed for predicting bioactive compounds, the prediction performances are diverse due to different methods and dataset. Therefore, there is urgent demand for an approach that connotes the previous methods and identify potential bioactive compounds with high accuracy. To meet the demand, we proposed a filtering strategy that identifies potential bioactive compounds by combining previously developed computational methods which predict ADMET, such as Human Intestinal Absorption (HIA) and Caco-2 permeability. Our approach was evaluated on 930 compounds that are known as bioactive compounds, which were extracted from literature, DrugBank and Dr. Dukes phytochemical databases. By applying our filtering strategy, 97.5% of the known bioactive compounds were correctly predicted as bioactive. We examined whether our approach can distinguish the potential bioactive compound from the non-potential bioactive compounds with Fishers' exact test, and a reasonable p-value (3.806 x 10-9) was derived. For the next step, we are planning to develop a machine-learning based method to improve our filtering approach.},
keywords = {ADME, Bioinformatics, Natural product},
pubstate = {published},
tppubtype = {conference}
}
Herbs consist of various chemical compounds. Thus, identifying potential bioactive compounds from those diversity is an important task for studies in the herb, food and natural products. Even though various computational approaches are developed for predicting bioactive compounds, the prediction performances are diverse due to different methods and dataset. Therefore, there is urgent demand for an approach that connotes the previous methods and identify potential bioactive compounds with high accuracy. To meet the demand, we proposed a filtering strategy that identifies potential bioactive compounds by combining previously developed computational methods which predict ADMET, such as Human Intestinal Absorption (HIA) and Caco-2 permeability. Our approach was evaluated on 930 compounds that are known as bioactive compounds, which were extracted from literature, DrugBank and Dr. Dukes phytochemical databases. By applying our filtering strategy, 97.5% of the known bioactive compounds were correctly predicted as bioactive. We examined whether our approach can distinguish the potential bioactive compound from the non-potential bioactive compounds with Fishers' exact test, and a reasonable p-value (3.806 x 10-9) was derived. For the next step, we are planning to develop a machine-learning based method to improve our filtering approach.
2014
1.
Suhyun Ha; Sunyong Yoo; Moonshik Shin; Jin Sook Kwak; Oran Kwon; Min Chang Choi; Keon Wook Kang; Hojung Nam; Doheon Lee
Abstract | Links | BibTeX | Dimensions | Tags: Ethnopharmacology, Natural product
@conference{ha2014integrative,
title = {Integrative Database for Exploring Compound Combinations of Natural Products for Medical Effects},
author = {Suhyun Ha and Sunyong Yoo and Moonshik Shin and Jin Sook Kwak and Oran Kwon and Min Chang Choi and Keon Wook Kang and Hojung Nam and Doheon Lee},
url = {https://dl.acm.org/doi/abs/10.1145/2665970.2665986},
doi = {10.1145/2665970.2665986},
year = {2014},
date = {2014-01-01},
urldate = {2014-01-01},
booktitle = {Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics},
pages = {41–41},
publisher = {CIKM},
abstract = {Natural products used in dietary supplements, complementary and alternative medicine (CAM) and conventional medicine are composites of multiple chemical compounds. These chemical compounds potentially offer an extensive source for drug discovery with accumulated knowledge of efficacy and safety. However, existing natural product related databases have drawbacks in both standardization and structuralization of information. Therefore, in this work, we construct an integrated database of natural products by mapping the prescription, herb, compound, and phenotype information to international identifiers and structuralizing the efficacy information through database integration and text-mining methods. We expect that the constructed database could serve as a fundamental resource for the natural products research.},
keywords = {Ethnopharmacology, Natural product},
pubstate = {published},
tppubtype = {conference}
}
Natural products used in dietary supplements, complementary and alternative medicine (CAM) and conventional medicine are composites of multiple chemical compounds. These chemical compounds potentially offer an extensive source for drug discovery with accumulated knowledge of efficacy and safety. However, existing natural product related databases have drawbacks in both standardization and structuralization of information. Therefore, in this work, we construct an integrated database of natural products by mapping the prescription, herb, compound, and phenotype information to international identifiers and structuralizing the efficacy information through database integration and text-mining methods. We expect that the constructed database could serve as a fundamental resource for the natural products research.