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AI in Drug Discovery

Edited by:

Igor Tetko, PhD, Helmholtz Munich, Germany
Djork-Arné Clevert, PhD, Pfizer, Germany

Submission Status: Closed 

This collection is no longer accepting submissions.

Journal of Cheminformatics is calling for submissions to our Collection on AI in Drug Discovery.

Image credit: © Katya Ahmad 

  1. This study investigates the risks of exposing confidential chemical structures when machine learning models trained on these structures are made publicly available. We use membership inference attacks, a commo...

    Authors: Fabian P. Krüger, Johan Östman, Lewis Mervin, Igor V. Tetko and Ola Engkvist
    Citation: Journal of Cheminformatics 2025 17:38
  2. Transformer-based, template-free SMILES-to-SMILES translation models for reaction prediction and single-step retrosynthesis are of interest to computer-aided synthesis planning systems, as they offer state-of-...

    Authors: Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber and Djork-Arné Clevert
    Citation: Journal of Cheminformatics 2025 17:31
  3. The link between in vitro hERG ion channel inhibition and subsequent in vivo QT interval prolongation, a critical risk factor for the development of arrythmias such as Torsade de Pointes, is so well establishe...

    Authors: Gregory W. Kyro, Matthew T. Martin, Eric D. Watt and Victor S. Batista
    Citation: Journal of Cheminformatics 2025 17:30
  4. In the drug discovery process, where experiments can be costly and time-consuming, computational models that predict drug-target interactions are valuable tools to accelerate the development of new therapeutic...

    Authors: Hannah Rosa Friesacher, Ola Engkvist, Lewis Mervin, Yves Moreau and Adam Arany
    Citation: Journal of Cheminformatics 2025 17:29
  5. Computer-aided drug design has the potential to significantly reduce the astronomical costs of drug development, and molecular docking plays a prominent role in this process. Molecular docking is an in silico tec...

    Authors: Andrew T. McNutt, Yanjing Li, Rocco Meli, Rishal Aggarwal and David Ryan Koes
    Citation: Journal of Cheminformatics 2025 17:28
  6. Retrosynthesis consists of recursively breaking down a target molecule to produce a synthesis route composed of readily accessible building blocks. In recent years, computer-aided synthesis planning methods ha...

    Authors: Paula Torren-Peraire, Jonas Verhoeven, Dorota Herman, Hugo Ceulemans, Igor V. Tetko and Jörg K. Wegner
    Citation: Journal of Cheminformatics 2025 17:26
  7. We evaluate the impact of pretraining Graph Transformer architectures on atom-level quantum-mechanical features for the modeling of absorption, distribution, metabolism, excretion, and toxicity (ADMET) propert...

    Authors: Alessio Fallani, Ramil Nugmanov, Jose Arjona-Medina, Jörg Kurt Wegner, Alexandre Tkatchenko and Kostiantyn Chernichenko
    Citation: Journal of Cheminformatics 2025 17:25
  8. Accurate prediction of ligand-receptor binding affinity is crucial in structure-based drug design, significantly impacting the development of effective drugs. Recent advances in machine learning (ML)–based sco...

    Authors: Farjana Tasnim Mukta, Md Masud Rana, Avery Meyer, Sally Ellingson and Duc D. Nguyen
    Citation: Journal of Cheminformatics 2025 17:10
  9. This article introduces StreamChol, a software for developing and applying mechanistic models to predict cholestasis. StreamChol is a Streamlit application, usable as a desktop application or web-accessible so...

    Authors: Pablo Rodríguez-Belenguer, Emilio Soria-Olivas and Manuel Pastor
    Citation: Journal of Cheminformatics 2025 17:9
  10. Effective light-based cancer treatments, such as photodynamic therapy (PDT) and photoactivated chemotherapy (PACT), rely on compounds that are activated by light efficiently, and absorb within the therapeutic ...

    Authors: V. Vigna, T. F. G. G. Cova, A. A. C. C. Pais and E. Sicilia
    Citation: Journal of Cheminformatics 2025 17:1
  11. Predicting protein-ligand binding affinity is essential for understanding protein-ligand interactions and advancing drug discovery. Recent research has demonstrated the advantages of sequence-based models and ...

    Authors: Guishen Wang, Hangchen Zhang, Mengting Shao, Yuncong Feng, Chen Cao and Xiaowen Hu
    Citation: Journal of Cheminformatics 2024 16:147
  12. Cardiotoxicity, particularly drug-induced arrhythmias, poses a significant challenge in drug development, highlighting the importance of early-stage prediction of human ether-a-go-go-related gene (hERG) toxici...

    Authors: Tianbiao Yang, Xiaoyu Ding, Elizabeth McMichael, Frank W. Pun, Alex Aliper, Feng Ren, Alex Zhavoronkov and Xiao Ding
    Citation: Journal of Cheminformatics 2024 16:143
  13. Hyperparameter optimization is very frequently employed in machine learning. However, an optimization of a large space of parameters could result in overfitting of models. In recent studies on solubility predi...

    Authors: Igor V. Tetko, Ruud van Deursen and Guillaume Godin
    Citation: Journal of Cheminformatics 2024 16:139
  14. Machine learning (ML) systems have enabled the modelling of quantitative structure–property relationships (QSPR) and structure-activity relationships (QSAR) using existing experimental data to predict target p...

    Authors: Yasmine Nahal, Janosch Menke, Julien Martinelli, Markus Heinonen, Mikhail Kabeshov, Jon Paul Janet, Eva Nittinger, Ola Engkvist and Samuel Kaski
    Citation: Journal of Cheminformatics 2024 16:138
  15. The exploration of chemical space holds promise for developing influential chemical entities. Molecular representations, which reflect features of molecular structure in silico, assist in navigating chemical s...

    Authors: Piao-Yang Cao, Yang He, Ming-Yang Cui, Xiao-Min Zhang, Qingye Zhang and Hong-Yu Zhang
    Citation: Journal of Cheminformatics 2024 16:133
  16. With the advent of artificial intelligence (AI), it is now possible to design diverse and novel molecules from previously unexplored chemical space. However, a challenge for chemists is the synthesis of such m...

    Authors: Sarveswara Rao Vangala, Sowmya Ramaswamy Krishnan, Navneet Bung, Dhandapani Nandagopal, Gomathi Ramasamy, Satyam Kumar, Sridharan Sankaran, Rajgopal Srinivasan and Arijit Roy
    Citation: Journal of Cheminformatics 2024 16:131
  17. Predicting protein-small molecule binding sites, the initial step in structure-guided drug design, remains challenging for proteins lacking experimentally derived ligand-bound structures. Here, we propose CLAP...

    Authors: Jue Wang, Yufan Liu and Boxue Tian
    Citation: Journal of Cheminformatics 2024 16:125

About the Collection

Journal of Cheminformatics is calling for submissions to our Collection on AI in Drug Discovery. 

The dramatic increase in the use of Artificial Intelligence (AI) and traditional machine learning methods in different scientific fields has become an essential asset in the future development of the chemical industry, including the pharmaceutical, agro biotech, and other chemical sectors. 

This Special Issue invites cutting-edge contributions in the rapidly evolving field of AI-driven drug discovery. We are seeking submissions encompassing various facets of the field, such as generative models, explainable AI, model distillation, uncertainty quantification, reaction informatics and synthetic route prediction, quantum machine learning for reactivity, methodologies for mining very large compound datasets, federated learning, analysis of HTS data and identification of frequent hitters, as well as other topics related to the use of machine learning (ML) in chemistry.  We look forward to receiving contributions from all researchers active in the field, whether they are developing novel methodologies or expanding the scope of established methodologies. A non-exhaustive list of topics includes:

●    Big Data and Advanced Machine Learning in Chemistry
●    Use of Deep Learning to Predict Molecular Properties
●    Modeling and Prediction of Chemical Reaction Data
●    eXplainable AI (XAI) in Chemistry 
●    Cheminformatics
●    Generative Models

The core collection will mainly consist of a selection of articles to be presented during the AIDD workshop “AI in Drug Discovery”  of the 33rd International Conference on Artificial Neural Networks (ICANN2024), which is co-organized by the European Neural Network Society and the Horizon2020 Marie Skłodowska-Curie Innovative Training Networks European Industrial Advanced machine learning for Innovative Drug Discovery (AIDD) as well as Horizon Europe Marie Skłodowska-Curie Doctoral Network Explainable AI for Molecules - AiChemist. Any authors participating in the ICANN2024 conference will receive a 20% discount on the APC fee. Authors that are not planning to participate in ICANN2024 are also welcome to submit to this Special Issue.

Submission Guidelines

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This Collection welcomes submission of research articles. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal. 

Articles for this Collection should be submitted via our submission system, Snapp. Please, select the appropriate Collection title “AI in Drug Discovery" under the “Details” tab during the submission stage.

Articles will undergo the journal’s standard peer-review process and are subject to all the journal’s standard policies. Articles will be added to the Collection as they are published.

The Editors have no competing interests with the submissions which they handle through the peer-review process. The peer-review of any submissions for which the Editors have competing interests is handled by another Editorial Board Member who has no competing interests.