Abstract
A number of machine learning (ML) approaches for drug discovery have been available that rely only on sequential (1D) and planar (2D) information without effectively using the 3D information for generating features of drugs. However, 3D information of small molecules can reflect relative position of atoms more directly, which affects molecular properties. In this work, we present a new deep learning model called Drug3D-DTI for drug-target interaction prediction. Drug3D-DTI takes advantage of molecular spatial information, i.e., atom proximity in three-dimensional (3D) structures. We comprehensively evaluated the performance of Drug3D-DTI on two datasets with two tasks of regression and classification. In particular, we compared Drug3D-DTI with several existing methods including the two cutting-edge methods for compound-protein interaction prediction. From the experimental results, Drug3D-DTI clearly outperformed other methods under all settings. Further, this performance improvement was validated by ablation experiments and a case study. The implementation of Drug3D-DTI is available at (https://github.com/zhiruiliao/Drug3D-DTI).
Original language | English |
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Title of host publication | Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021 |
Editors | Yufei Huang, Lukasz Kurgan, Feng Luo, Xiaohua Tony Hu, Yidong Chen, Edward Dougherty, Andrzej Kloczkowski, Yaohang Li |
Publisher | IEEE |
Pages | 340-347 |
Number of pages | 8 |
ISBN (Electronic) | 9781665401265 |
ISBN (Print) | 9781665429825 |
DOIs | |
Publication status | Published - 14 Jan 2022 |
Event | IEEE International Conference on Bioinformatics and Biomedicine 2021: IEEE BIBM 2021 - Online Duration: 09 Dec 2021 → 12 Dec 2021 https://ieeebibm.org/BIBM2021/ https://ieeebibm.org/BIBM2021/BIBM%202021%20Program%20-%20Dec%209.pdf (Program) https://ieeexplore.ieee.org/xpl/conhome/9669261/proceeding (Proceedings) |
Publication series
Name | Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021 |
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Conference
Conference | IEEE International Conference on Bioinformatics and Biomedicine 2021 |
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Period | 09/12/21 → 12/12/21 |
Other | The IEEE International Conference on Bioinformatics and Biomedicine (BIBM) has established itself as the premier research conference in bioinformatics and biomedicine. IEEE BIBM 2021 provides a leading forum for disseminating the latest research in bioinformatics and health informatics. It brings together academic and industrial scientists from computer science, biology, chemistry, medicine, mathematics and statistics. We solicit high-quality original research papers (including significant work-in-progress) in any aspect of bioinformatics, genomics, and biomedicine. New computational techniques and methods and their application in life science and medical domains are especially encouraged. |
Internet address |