FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction
Many efforts have been exerted toward screening potential drugs for targets, and conducting wet experiments remains a laborious and time-consuming approach. Artificial intelligence methods, such as Convolutional Neural Network (CNN), are widely used to facilitate new drug discovery. Owing to the str...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Tsinghua University Press
2023-03-01
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| Series: | Big Data Mining and Analytics |
| Subjects: | |
| Online Access: | https://www.sciopen.com/article/10.26599/BDMA.2022.9020005 |
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| author | Xuekai Zhu Juan Liu Jian Zhang Zhihui Yang Feng Yang Xiaolei Zhang |
| author_facet | Xuekai Zhu Juan Liu Jian Zhang Zhihui Yang Feng Yang Xiaolei Zhang |
| author_sort | Xuekai Zhu |
| collection | DOAJ |
| description | Many efforts have been exerted toward screening potential drugs for targets, and conducting wet experiments remains a laborious and time-consuming approach. Artificial intelligence methods, such as Convolutional Neural Network (CNN), are widely used to facilitate new drug discovery. Owing to the structural limitations of CNN, features extracted from this method are local patterns that lack global information. However, global information extracted from the whole sequence and local patterns extracted from the special domain can influence the drug-target affinity. A fusion of global information and local patterns can construct neural network calculations closer to actual biological processes. This paper proposes a Fingerprint-embedding framework for Drug-Target binding Affinity prediction (FingerDTA), which uses CNN to extract local patterns and utilize fingerprints to characterize global information. These fingerprints are generated on the basis of the whole sequence of drugs or targets. Furthermore, FingerDTA achieves comparable performance on Davis and KIBA data sets. In the case study of screening potential drugs for the spike protein of the coronavirus disease 2019 (COVID-19), 7 of the top 10 drugs have been confirmed potential by literature. Ultimately, the docking experiment demonstrates that FingerDTA can find novel drug candidates for targets. All codes are available at http://lanproxy.biodwhu.cn:9099/mszjaas/FingerDTA.git. |
| format | Article |
| id | doaj-art-ee156446775e432c8f3fcde6a66d84b0 |
| institution | Kabale University |
| issn | 2096-0654 |
| language | English |
| publishDate | 2023-03-01 |
| publisher | Tsinghua University Press |
| record_format | Article |
| series | Big Data Mining and Analytics |
| spelling | doaj-art-ee156446775e432c8f3fcde6a66d84b02025-02-02T13:35:59ZengTsinghua University PressBig Data Mining and Analytics2096-06542023-03-016111010.26599/BDMA.2022.9020005FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity PredictionXuekai Zhu0Juan Liu1Jian Zhang2Zhihui Yang3Feng Yang4Xiaolei Zhang5School of Computer Science, Wuhan University, Wuhan 430072, ChinaSchool of Computer Science, Wuhan University, Wuhan 430072, ChinaSchool of Computer Science, Wuhan University, Wuhan 430072, ChinaSchool of Computer Science, Wuhan University, Wuhan 430072, ChinaSchool of Computer Science, Wuhan University, Wuhan 430072, ChinaSchool of Computer Science, Wuhan University, Wuhan 430072, ChinaMany efforts have been exerted toward screening potential drugs for targets, and conducting wet experiments remains a laborious and time-consuming approach. Artificial intelligence methods, such as Convolutional Neural Network (CNN), are widely used to facilitate new drug discovery. Owing to the structural limitations of CNN, features extracted from this method are local patterns that lack global information. However, global information extracted from the whole sequence and local patterns extracted from the special domain can influence the drug-target affinity. A fusion of global information and local patterns can construct neural network calculations closer to actual biological processes. This paper proposes a Fingerprint-embedding framework for Drug-Target binding Affinity prediction (FingerDTA), which uses CNN to extract local patterns and utilize fingerprints to characterize global information. These fingerprints are generated on the basis of the whole sequence of drugs or targets. Furthermore, FingerDTA achieves comparable performance on Davis and KIBA data sets. In the case study of screening potential drugs for the spike protein of the coronavirus disease 2019 (COVID-19), 7 of the top 10 drugs have been confirmed potential by literature. Ultimately, the docking experiment demonstrates that FingerDTA can find novel drug candidates for targets. All codes are available at http://lanproxy.biodwhu.cn:9099/mszjaas/FingerDTA.git.https://www.sciopen.com/article/10.26599/BDMA.2022.9020005drug-target binding affinityfingerprintnew drug discovery |
| spellingShingle | Xuekai Zhu Juan Liu Jian Zhang Zhihui Yang Feng Yang Xiaolei Zhang FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction Big Data Mining and Analytics drug-target binding affinity fingerprint new drug discovery |
| title | FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction |
| title_full | FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction |
| title_fullStr | FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction |
| title_full_unstemmed | FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction |
| title_short | FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction |
| title_sort | fingerdta a fingerprint embedding framework for drug target binding affinity prediction |
| topic | drug-target binding affinity fingerprint new drug discovery |
| url | https://www.sciopen.com/article/10.26599/BDMA.2022.9020005 |
| work_keys_str_mv | AT xuekaizhu fingerdtaafingerprintembeddingframeworkfordrugtargetbindingaffinityprediction AT juanliu fingerdtaafingerprintembeddingframeworkfordrugtargetbindingaffinityprediction AT jianzhang fingerdtaafingerprintembeddingframeworkfordrugtargetbindingaffinityprediction AT zhihuiyang fingerdtaafingerprintembeddingframeworkfordrugtargetbindingaffinityprediction AT fengyang fingerdtaafingerprintembeddingframeworkfordrugtargetbindingaffinityprediction AT xiaoleizhang fingerdtaafingerprintembeddingframeworkfordrugtargetbindingaffinityprediction |