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  1. The applicability domain of machine learning models trained on structural fingerprints for the prediction of biological endpoints is often limited by the lack of diversity of chemical space of the training dat...

    Authors: Srijit Seal, Hongbin Yang, Maria-Anna Trapotsi, Satvik Singh, Jordi Carreras-Puigvert, Ola Spjuth and Andreas Bender
    Citation: Journal of Cheminformatics 2023 15:56
  2. Tokenization is an important preprocessing step in natural language processing that may have a significant influence on prediction quality. This research showed that the traditional SMILES tokenization has a c...

    Authors: Umit V. Ucak, Islambek Ashyrmamatov and Juyong Lee
    Citation: Journal of Cheminformatics 2023 15:55

    The Correction to this article has been published in Journal of Cheminformatics 2023 15:70

  3. Accurate prediction of molecular properties is essential in the screening and development of drug molecules and other functional materials. Traditionally, property-specific molecular descriptors are used in ma...

    Authors: Rajarshi Guha and Darrell Velegol
    Citation: Journal of Cheminformatics 2023 15:54
  4. Predicting in advance the behavior of new chemical compounds can support the design process of new products by directing the research toward the most promising candidates and ruling out others. Such predictive...

    Authors: Katharina Dost, Zac Pullar-Strecker, Liam Brydon, Kunyang Zhang, Jasmin Hafner, Patricia J. Riddle and Jörg S. Wicker
    Citation: Journal of Cheminformatics 2023 15:53
  5. Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and acc...

    Authors: Eftychia E. Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer, Timo Sachsenberg, Omkar S. Mohite, Matin Nuhamunada, Oliver Kohlbacher and Tilmann Weber
    Citation: Journal of Cheminformatics 2023 15:52
  6. Drug resistance represents a major obstacle to therapeutic innovations and is a prevalent feature in prostate cancer (PCa). Androgen receptors (ARs) are the hallmark therapeutic target for prostate cancer modu...

    Authors: Nalini Schaduangrat, Nuttapat Anuwongcharoen, Phasit Charoenkwan and Watshara Shoombuatong
    Citation: Journal of Cheminformatics 2023 15:50
  7. It is insightful to report an estimator that describes how certain a model is in a prediction, additionally to the prediction alone. For regression tasks, most approaches implement a variation of the ensemble ...

    Authors: Thomas-Martin Dutschmann, Lennart Kinzel, Antonius ter Laak and Knut Baumann
    Citation: Journal of Cheminformatics 2023 15:49
  8. Identification and validation of bioactive small-molecule targets is a significant challenge in drug discovery. In recent years, various in-silico approaches have been proposed to expedite time- and resource-cons...

    Authors: Su-Qing Yang, Liu-Xia Zhang, You-Jin Ge, Jin-Wei Zhang, Jian-Xin Hu, Cheng-Ying Shen, Ai-Ping Lu, Ting-Jun Hou and Dong-Sheng Cao
    Citation: Journal of Cheminformatics 2023 15:48
  9. Pairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their binding affinity for a given target are known as activity cliffs (ACs). It has been hypoth...

    Authors: Markus Dablander, Thierry Hanser, Renaud Lambiotte and Garrett M. Morris
    Citation: Journal of Cheminformatics 2023 15:47
  10. Efficient and machine-readable representations are needed to accurately identify, validate and communicate information of chemical structures. Many such representations have been developed (as, for example, th...

    Authors: Kostas Blekos, Kostas Chairetakis, Iseult Lynch and Effie Marcoulaki
    Citation: Journal of Cheminformatics 2023 15:44
  11. Artificial intelligence has deeply revolutionized the field of medicinal chemistry with many impressive applications, but the success of these applications requires a massive amount of training samples with hi...

    Authors: Kexin Chen, Guangyong Chen, Junyou Li, Yuansheng Huang, Ercheng Wang, Tingjun Hou and Pheng-Ann Heng
    Citation: Journal of Cheminformatics 2023 15:43
  12. Artificial intelligence (AI)-based molecular design methods, especially deep generative models for generating novel molecule structures, have gratified our imagination to explore unknown chemical space without...

    Authors: Xiaohong Liu, Wei Zhang, Xiaochu Tong, Feisheng Zhong, Zhaojun Li, Zhaoping Xiong, Jiacheng Xiong, Xiaolong Wu, Zunyun Fu, Xiaoqin Tan, Zhiguo Liu, Sulin Zhang, Hualiang Jiang, Xutong Li and Mingyue Zheng
    Citation: Journal of Cheminformatics 2023 15:42
  13. Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to identify similar structures. Here we report an open-source c...

    Authors: Sascha Jung, Helge Vatheuer and Paul Czodrowski
    Citation: Journal of Cheminformatics 2023 15:40
  14. High throughput screening (HTS) is widely used in drug discovery and chemical biology to identify and characterize agents having pharmacologic properties often by evaluation of large chemical libraries. Standa...

    Authors: Bryan Queme, John C. Braisted, Patricia Dranchak and James Inglese
    Citation: Journal of Cheminformatics 2023 15:39
  15. Drug discovery for a protein target is a laborious and costly process. Deep learning (DL) methods have been applied to drug discovery and successfully generated novel molecular structures, and they can substan...

    Authors: Yangyang Chen, Zixu Wang, Lei Wang, Jianmin Wang, Pengyong Li, Dongsheng Cao, Xiangxiang Zeng, Xiucai Ye and Tetsuya Sakurai
    Citation: Journal of Cheminformatics 2023 15:38
  16. Vibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs ...

    Authors: Jonathan Lam, Richard J. Lewis and Jonathan M. Goodman
    Citation: Journal of Cheminformatics 2023 15:36
  17. Chemical mutagenicity is a serious issue that needs to be addressed in early drug discovery. Over a long period of time, medicinal chemists have manually summarized a series of empirical rules for the optimiza...

    Authors: Chaofeng Lou, Hongbin Yang, Hua Deng, Mengting Huang, Weihua Li, Guixia Liu, Philip W. Lee and Yun Tang
    Citation: Journal of Cheminformatics 2023 15:35
  18. Toxicological evaluation of substances in regulation still often relies on animal experiments. Understanding the substances’ mode-of-action is crucial to develop alternative test strategies. Omics methods are ...

    Authors: Aileen Bahl, Celine Ibrahim, Kristina Plate, Andrea Haase, Jörn Dengjel, Penny Nymark and Verónica I. Dumit
    Citation: Journal of Cheminformatics 2023 15:34
  19. Drug combination therapies are promising clinical treatments for curing patients. However, efficiently identifying valid drug combinations remains challenging because the number of available drugs has increase...

    Authors: Mengdie Xu, Xinwei Zhao, Jingyu Wang, Wei Feng, Naifeng Wen, Chunyu Wang, Junjie Wang, Yun Liu and Lingling Zhao
    Citation: Journal of Cheminformatics 2023 15:33
  20. Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid chromatography-mass spectrometry (LC–MS) to achieve a high-thro...

    Authors: Mahnoor Zulfiqar, Luiz Gadelha, Christoph Steinbeck, Maria Sorokina and Kristian Peters
    Citation: Journal of Cheminformatics 2023 15:32
  21. Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding affinity and thus impact the drug’s efficacy and side effects...

    Authors: Ammar Ammar, Rachel Cavill, Chris Evelo and Egon Willighagen
    Citation: Journal of Cheminformatics 2023 15:31
  22. Graph convolutional neural networks (GCNs) have been repeatedly shown to have robust capacities for modeling graph data such as small molecules. Message-passing neural networks (MPNNs), a group of GCN variants...

    Authors: Chengyou Liu, Yan Sun, Rebecca Davis, Silvia T. Cardona and Pingzhao Hu
    Citation: Journal of Cheminformatics 2023 15:29
  23. Non-target analysis combined with liquid chromatography high resolution mass spectrometry is considered one of the most comprehensive strategies for the detection and identification of known and unknown chemic...

    Authors: Jim Boelrijk, Denice van Herwerden, Bernd Ensing, Patrick Forré and Saer Samanipour
    Citation: Journal of Cheminformatics 2023 15:28
  24. The simplified molecular-input line-entry system (SMILES) is the most prevalent molecular representation used in AI-based chemical applications. However, there are innate limitations associated with the intern...

    Authors: Umit V. Ucak, Islambek Ashyrmamatov and Juyong Lee
    Citation: Journal of Cheminformatics 2023 15:26

    The Correction to this article has been published in Journal of Cheminformatics 2023 15:68

  25. Published reports of chemical compounds often contain multiple machine-readable descriptions which may supplement each other in order to yield coherent and complete chemical representations. This publication p...

    Authors: Andrius Merkys, Antanas Vaitkus, Algirdas Grybauskas, Aleksandras Konovalovas, Miguel Quirós and Saulius Gražulis
    Citation: Journal of Cheminformatics 2023 15:25
  26. Rational drug design often starts from specific scaffolds to which side chains/substituents are added or modified due to the large drug-like chemical space available to search for novel drug-like molecules. Wi...

    Authors: Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman and Gerard J. P. van Westen
    Citation: Journal of Cheminformatics 2023 15:24
  27. The influence of molecular fragmentation and parameter settings on a mesoscopic dissipative particle dynamics (DPD) simulation of lamellar bilayer formation for a C10E4/water mixture is studied. A “bottom-up” dec...

    Authors: Felix Bänsch, Christoph Steinbeck and Achim Zielesny
    Citation: Journal of Cheminformatics 2023 15:23
  28. Generative deep learning models have emerged as a powerful approach for de novo drug design as they aid researchers in finding new molecules with desired properties. Despite continuous improvements in the fiel...

    Authors: Linde Schoenmaker, Olivier J. M. Béquignon, Willem Jespers and Gerard J. P. van Westen
    Citation: Journal of Cheminformatics 2023 15:22
  29. Artificial Intelligence is revolutionizing many aspects of the pharmaceutical industry. Deep learning models are now routinely applied to guide drug discovery projects leading to faster and improved findings, ...

    Authors: Paulo Neves, Kelly McClure, Jonas Verhoeven, Natalia Dyubankova, Ramil Nugmanov, Andrey Gedich, Sairam Menon, Zhicai Shi and Jörg K. Wegner
    Citation: Journal of Cheminformatics 2023 15:20

    The Correction to this article has been published in Journal of Cheminformatics 2023 15:30

  30. Particle-Based (PB) simulations, including Molecular Dynamics (MD), provide access to system observables that are not easily available experimentally. However, in most cases, PB data needs to be processed afte...

    Authors: Samuel Tovey, Fabian Zills, Francisco Torres-Herrador, Christoph Lohrmann, Marco Brückner and Christian Holm
    Citation: Journal of Cheminformatics 2023 15:19
  31. Citations are an essential aspect of research communication and have become the basis of many evaluation metrics in the academic world. Some see citation counts as a mark of scientific impact or even quality, ...

    Authors: Egon Willighagen
    Citation: Journal of Cheminformatics 2023 15:14

    The Editorial to this article has been published in Journal of Cheminformatics 2023 15:15

  32. Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mut...

    Authors: Mingchen Li, Liqi Kang, Yi Xiong, Yu Guang Wang, Guisheng Fan, Pan Tan and Liang Hong
    Citation: Journal of Cheminformatics 2023 15:12
  33. In this work, we provide further development of the junction tree variational autoencoder (JT VAE) architecture in terms of implementation and application of the internal feature space of the model. Pretrainin...

    Authors: Vladimir Kondratyev, Marian Dryzhakov, Timur Gimadiev and Dmitriy Slutskiy
    Citation: Journal of Cheminformatics 2023 15:11
  34. This article documents enu, a freely-downloadable, open-source and stand-alone program written in C++ for the enumeration of the constitutional isomers and stereoisomers of a molecular formula. The program relies...

    Authors: Salomé R. Rieder, Marina P. Oliveira, Sereina Riniker and Philippe H. Hünenberger
    Citation: Journal of Cheminformatics 2023 15:10
  35. The field of high-resolution mass spectrometry (HRMS) and ancillary hyphenated techniques comprise a rapidly expanding and evolving area. As popularity of HRMS instruments grows, there is a concurrent need for...

    Authors: Dane R. Letourneau, Dennis D. August and Dietrich A. Volmer
    Citation: Journal of Cheminformatics 2023 15:7