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Implementation of Ensemble Methods on Classification of CDK2 Inhibitor as Anti-Cancer Agent

IJCCS (Indonesian Journal of Computing and Cybernetics Systems) · Vol. 17 No. 1 (2023) · pp. 11–22

DOI
10.22146/ijccs.78537
ISSN
2460-7258, 1978-1520
Published
2023-02-23
Publisher
IndoCEISS in colaboration with Universitas Gadjah Mada, Indonesia.
Language
eng
License
creativecommons.org/licenses/by-sa/4.0

Abstract

Cancer is known as the second leading cause of death worldwide. About 7-10 million cases of death by cancer occur every year. The recent treatment to heal the cancer is chemotherapy. However, chemotherapy treatment is known to have side effects and cell resistance issues to certain drugs. Therefore, it is required to develop a new drug that can reduce the side effects and provide a better treatment effect. In general, anti-cancer drugs are developed by targeting Cyclin-Dependent Kinase 2 (CDK2) enzyme. Conventional drug design is not effective and efficient for obtaining new drug candidates because of no information about the biological activity before it is synthesized. In this study, we aim to develop a model to predict the activity of CDK2 inhibitors by using ensemble methods, i.e., XGBoost, Random Forest, and AdaBoost. The study was conducted by calculating several fingerprints, i.e., Estate, Extended, Maccs, and Pubchem, as feature variables. Based on the results, we found that Random Forest with Pubchem fingerprint gives the best result with the value of Matthews Correlation Coefficient (MCC) and Area Under the ROC Curve (AUC) values are 0.979 and 0.999, respectively. From this study, we contributed to revealing the potency of the ensemble with fingerprint in bioactivity prediction, especially CDK2 inhibitors as anti-cancer agents.

Keywords

Collaboration network of the authors

6 authors · 9 co-authorship links · 3 across different organisations

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  • Telkom University
  • Bandung Institute of Technology
  • Different organisations
  • Same organisation
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Co-authorOrganisationJoint articles
Dwi Hendratmo WidyantoroBandung Institute of Technology1
Kridanto SurendroBandung Institute of Technology1

Affiliations come from OpenAlex; journal OAI-PMH metadata carries none. Authors without an OpenAlex ID are matched by name, which can merge or split people.

Metadata source: OAI-PMH (metadata jurnal) https://journal.ugm.ac.id/ijccs/oai, first harvested 26 Okt 2026, last seen 26 Okt 2026.
Original metadata (oai_dc) 
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	<dc:title xml:lang="en-US">Implementation of Ensemble Methods on Classification of CDK2 Inhibitor as Anti-Cancer Agent</dc:title>
	<dc:creator>Kurniawan, Isman</dc:creator>
	<dc:creator>Anggraini, Mela Mai</dc:creator>
	<dc:creator>Aditsania, Annisa</dc:creator>
	<dc:creator>Setiawan, Erwin Budi</dc:creator>
	<dc:subject xml:lang="en-US"></dc:subject>
	<dc:subject xml:lang="en-US">QSAR; CDK2; XGBoost; random forest; AdaBoost</dc:subject>
	<dc:description xml:lang="en-US">Cancer is known as the second leading cause of death worldwide. About 7-10 million cases of death by cancer occur every year. The recent treatment to heal the cancer is chemotherapy. However, chemotherapy treatment is known to have side effects and cell resistance issues to certain drugs. Therefore, it is required to develop a new drug that can reduce the side effects and provide a better treatment effect. In general, anti-cancer drugs are developed by targeting Cyclin-Dependent Kinase 2 (CDK2) enzyme. Conventional drug design is not effective and efficient for obtaining new drug candidates because of no information about the biological activity before it is synthesized. In this study, we aim to develop a model to predict the activity of CDK2 inhibitors by using ensemble methods, i.e.,  XGBoost, Random Forest, and AdaBoost. The study was conducted by calculating several fingerprints, i.e., Estate, Extended, Maccs, and Pubchem, as feature variables. Based on the results, we found that Random Forest with Pubchem fingerprint gives the best result with the value of Matthews Correlation Coefficient (MCC) and Area Under the ROC Curve (AUC) values are 0.979 and 0.999, respectively. From this study, we contributed to revealing the potency of the ensemble with fingerprint in bioactivity prediction, especially CDK2 inhibitors as anti-cancer agents.</dc:description>
	<dc:publisher xml:lang="en-US">IndoCEISS in colaboration with Universitas Gadjah Mada, Indonesia.</dc:publisher>
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	<dc:date>2023-02-23</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
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	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://journal.ugm.ac.id/ijccs/article/view/78537</dc:identifier>
	<dc:identifier>10.22146/ijccs.78537</dc:identifier>
	<dc:source xml:lang="en-US">IJCCS (Indonesian Journal of Computing and Cybernetics Systems); Vol 17, No 1 (2023): January; 11-22</dc:source>
	<dc:source>2460-7258</dc:source>
	<dc:source>1978-1520</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://journal.ugm.ac.id/ijccs/article/view/78537/35775</dc:relation>
	<dc:rights xml:lang="en-US">Copyright (c) 2023 IJCCS (Indonesian Journal of Computing and Cybernetics Systems)</dc:rights>
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