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Artificial Intelligence in Drug Design: Opportunities and Challenges

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (1 December 2023) | Viewed by 2603

Special Issue Editors

Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
Interests: artificial intelligence; machine learning; deep learning; chemoinformatics; drug design; systems biology; single cell multiomics

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Guest Editor
Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi), New Delhi 110020, India
Interests: ML and DL approaches for druggability prediction; QM fragmentation based approaches for druggability prediction; parallel virtual screening in HPCs and GPUs for accelerated drugs discovery; flexible docking assisted drugs discovery; atomistic simulation of virus-host cell interaction

Special Issue Information

Dear Colleagues,

In traditional methods of drug design, searching for a drug in a haystack that exhibits desired biological activities while conforming to safe pharmacological profiles can be long, costly, and challenging tasks. Recent advances in artificial intelligence (AI) have brought a revolution in today’s drug discovery process, ranging from target identification and lead searching, to safety profile prediction. Computational techniques, such as chemoinformatics, can be used to extract meaningful features from chemical structures of large compound databases. In conjunction with machine learning models, quantitative structure–activity relationships (QSARs) can be established to infer new drug activity, inverse drug design, and drug repurposing. Recent rises in deep learning and generative AI also saw their wide applicability in protein structure prediction, functional site identification, structure-based drug design (SBDD), and ligand-based drug design (LBDD). System-level information from clinical data and high-throughput experiments can likewise be leveraged via data-driven ways to minimize drug toxicity and accelerate drug approval. In recognition of the increasing influences of AI in drug design, researchers and drug designers from academia and the pharmaceutical industry are invited to contribute to this special Issue titled, “Artificial Intelligence in Drug Design: Opportunities and Challenges” to guide future development in this emerging field.

Dr. Yu-Chen Lo
Dr. Natarajan Arul Murugan 
Guest Editors

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Keywords

  • artificial intelligence
  • machine learning
  • deep learning
  • chemoinformatics
  • drug design
  • systems biology bioinformatics multiomics

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Published Papers (1 paper)

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Research

16 pages, 3953 KiB  
Article
An Augmented Sample Selection Framework for Prediction of Anticancer Peptides
by Huawei Tao, Shuai Shan, Hongliang Fu, Chunhua Zhu and Boye Liu
Molecules 2023, 28(18), 6680; https://doi.org/10.3390/molecules28186680 - 18 Sep 2023
Cited by 4 | Viewed by 1697
Abstract
Anticancer peptides (ACPs) have promising prospects for cancer treatment. Traditional ACP identification experiments have the limitations of low efficiency and high cost. In recent years, data-driven deep learning techniques have shown significant potential for ACP prediction. However, data-driven prediction models rely heavily on [...] Read more.
Anticancer peptides (ACPs) have promising prospects for cancer treatment. Traditional ACP identification experiments have the limitations of low efficiency and high cost. In recent years, data-driven deep learning techniques have shown significant potential for ACP prediction. However, data-driven prediction models rely heavily on extensive training data. Furthermore, the current publicly accessible ACP dataset is limited in size, leading to inadequate model generalization. While data augmentation effectively expands dataset size, existing techniques for augmenting ACP data often generate noisy samples, adversely affecting prediction performance. Therefore, this paper proposes a novel augmented sample selection framework for the prediction of anticancer peptides (ACPs-ASSF). First, the prediction model is trained using raw data. Then, the augmented samples generated using the data augmentation technique are fed into the trained model to compute pseudo-labels and estimate the uncertainty of the model prediction. Finally, samples with low uncertainty, high confidence, and pseudo-labels consistent with the original labels are selected and incorporated into the training set to retrain the model. The evaluation results for the ACP240 and ACP740 datasets show that ACPs-ASSF achieved accuracy improvements of up to 5.41% and 5.68%, respectively, compared to the traditional data augmentation method. Full article
(This article belongs to the Special Issue Artificial Intelligence in Drug Design: Opportunities and Challenges)
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