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  1. Application of chemical named entity recognition (CNER) algorithms allows retrieval of information from texts about chemical compound identifiers and creates associations with physical–chemical properties and ...

    Authors: O. A. Tarasova, A. V. Rudik, N. Yu. Biziukova, D. A. Filimonov and V. V. Poroikov
    Citation: Journal of Cheminformatics 2022 14:55
  2. Machine learning (ML) models require an extensive, user-driven selection of molecular descriptors in order to learn from chemical structures to predict actives and inactives with a high reliability. In additio...

    Authors: Aljoša Smajić, Melanie Grandits and Gerhard F. Ecker
    Citation: Journal of Cheminformatics 2022 14:54
  3. Recently, graph neural networks (GNNs) have revolutionized the field of chemical property prediction and achieved state-of-the-art results on benchmark data sets. Compared with the traditional descriptor- and ...

    Authors: Yue Kong, Xiaoman Zhao, Ruizi Liu, Zhenwu Yang, Hongyan Yin, Bowen Zhao, Jinling Wang, Bingjie Qin and Aixia Yan
    Citation: Journal of Cheminformatics 2022 14:52
  4. In virtual screening for drug discovery, hit enrichment curves are widely used to assess the performance of ranking algorithms with regard to their ability to identify early enrichment. Unfortunately, research...

    Authors: Jeremy R Ash and Jacqueline M Hughes-Oliver
    Citation: Journal of Cheminformatics 2022 14:50
  5. Polypharmacy refers to the administration of multiple drugs on a daily basis. It has demonstrated effectiveness in treating many complex diseases , but it has a higher risk of adverse drug reactions. Hence, th...

    Authors: Nina Lukashina, Elena Kartysheva, Ola Spjuth, Elizaveta Virko and Aleksei Shpilman
    Citation: Journal of Cheminformatics 2022 14:49
  6. Comparing chemical structures to infer protein targets and functions is a common approach, but basing comparisons on chemical similarity alone can be misleading. Here we present a methodology for predicting ta...

    Authors: Akshai P. Sreenivasan, Philip J Harrison, Wesley Schaal, Damian J. Matuszewski, Kim Kultima and Ola Spjuth
    Citation: Journal of Cheminformatics 2022 14:47
  7. UDP-glucuronosyltransferases (UGTs) have gained increasing attention as they play important roles in the phase II metabolism of drugs. Due to the time-consuming process and high cost of experimental approaches...

    Authors: Mengting Huang, Chaofeng Lou, Zengrui Wu, Weihua Li, Philip W. Lee, Yun Tang and Guixia Liu
    Citation: Journal of Cheminformatics 2022 14:46
  8. Bitterness is an aversive cue elicited by thousands of chemically diverse compounds. Bitter taste may prevent consumption of foods and jeopardize drug compliance. The G protein-coupled receptors for bitter tas...

    Authors: Eitan Margulis, Yuli Slavutsky, Tatjana Lang, Maik Behrens, Yuval Benjamini and Masha Y. Niv
    Citation: Journal of Cheminformatics 2022 14:45
  9. Blood–brain barrier is a pivotal factor to be considered in the process of central nervous system (CNS) drug development, and it is of great significance to rapidly explore the blood–brain barrier permeability...

    Authors: Xiaochu Tong, Dingyan Wang, Xiaoyu Ding, Xiaoqin Tan, Qun Ren, Geng Chen, Yu Rong, Tingyang Xu, Junzhou Huang, Hualiang Jiang, Mingyue Zheng and Xutong Li
    Citation: Journal of Cheminformatics 2022 14:44
  10. Drug design is an important area of study for pharmaceutical businesses. However, low efficacy, off-target delivery, time consumption, and high cost are challenges and can create barriers that impact this proc...

    Authors: Maryam Abbasi, Beatriz P. Santos, Tiago C. Pereira, Raul Sofia, Nelson R. C. Monteiro, Carlos J. V. Simões, Rui M. M. Brito, Bernardete Ribeiro, José L. Oliveira and Joel P. Arrais
    Citation: Journal of Cheminformatics 2022 14:40

    The Correction to this article has been published in Journal of Cheminformatics 2022 14:53

  11. Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication re...

    Authors: Bienfait K. Isamura and Kevin A. Lobb
    Citation: Journal of Cheminformatics 2022 14:39
  12. As an alternative to one drug-one target approaches, systems biology methods can provide a deeper insight into the holistic effects of drugs. Network-based approaches are tools of systems biology, that can rep...

    Authors: Barbara Füzi, Rahuman S. Malik-Sheriff, Emma J. Manners, Henning Hermjakob and Gerhard F. Ecker
    Citation: Journal of Cheminformatics 2022 14:37
  13. The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over...

    Authors: Henning Otto Brinkhaus, Achim Zielesny, Christoph Steinbeck and Kohulan Rajan
    Citation: Journal of Cheminformatics 2022 14:36
  14. Facing the continuous emergence of new psychoactive substances (NPS) and their threat to public health, more effective methods for NPS prediction and identification are critical. In this study, the pharmacolog...

    Authors: Kedan He
    Citation: Journal of Cheminformatics 2022 14:35

    The Correction to this article has been published in Journal of Cheminformatics 2022 14:42

  15. As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical r...

    Authors: Barbara R. Terlouw, Sophie P. J. M. Vromans and Marnix H. Medema
    Citation: Journal of Cheminformatics 2022 14:34
  16. Retention time information is used for metabolite annotation in metabolomic experiments. But its usefulness is hindered by the availability of experimental retention time data in metabolomic databases, and by ...

    Authors: Constantino A. García, Alberto Gil-de-la-Fuente, Coral Barbas and Abraham Otero
    Citation: Journal of Cheminformatics 2022 14:33
  17. Recently, imputation techniques have been adapted to predict activity values among sparse bioactivity matrices, showing improvements in predictive performance over traditional QSAR models. These models are abl...

    Authors: Moritz Walter, Luke N. Allen, Antonio de la Vega de León, Samuel J. Webb and Valerie J. Gillet
    Citation: Journal of Cheminformatics 2022 14:32
  18. The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The diversity of the features in the training data ...

    Authors: Henning Otto Brinkhaus, Kohulan Rajan, Achim Zielesny and Christoph Steinbeck
    Citation: Journal of Cheminformatics 2022 14:31
  19. Natural products (NPs) are a valuable source for anti-inflammatory drug discovery. However, they are limited by the unpredictability of the structures and functions. Therefore, computational and data-driven pr...

    Authors: Ruihan Zhang, Shoupeng Ren, Qi Dai, Tianze Shen, Xiaoli Li, Jin Li and Weilie Xiao
    Citation: Journal of Cheminformatics 2022 14:30
  20. Integration of medicinal chemistry data from numerous public resources is an increasingly important part of academic drug discovery and translational research because it can bring a wealth of important knowled...

    Authors: Daniela Dolciami, Eloy Villasclaras-Fernandez, Christos Kannas, Mirco Meniconi, Bissan Al-Lazikani and Albert A. Antolin
    Citation: Journal of Cheminformatics 2022 14:28
  21. Unpredicted drug safety issues constitute the majority of failures in the pharmaceutical industry according to several studies. Some of these preclinical safety issues could be attributed to the non-selective ...

    Authors: Doha Naga, Wolfgang Muster, Eunice Musvasva and Gerhard F. Ecker
    Citation: Journal of Cheminformatics 2022 14:27
  22. Chemical structure generators are used in cheminformatics to produce or enumerate virtual molecules based on a set of boundary conditions. The result can then be tested for properties of interest, such as adhe...

    Authors: Brendan D. McKay, Mehmet Aziz Yirik and Christoph Steinbeck
    Citation: Journal of Cheminformatics 2022 14:24
  23. Drug–drug interaction (DDI) often causes serious adverse reactions and thus results in inestimable economic and social loss. Currently, comprehensive DDI evaluation has become a major challenge in pharmaceutic...

    Authors: Ning-Ning Wang, Xiang-Gui Wang, Guo-Li Xiong, Zi-Yi Yang, Ai-Ping Lu, Xiang Chen, Shao Liu, Ting-Jun Hou and Dong-Sheng Cao
    Citation: Journal of Cheminformatics 2022 14:23
  24. We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, includ...

    Authors: Simon Bray, Tim Dudgeon, Rachael Skyner, Rolf Backofen, Björn Grüning and Frank von Delft
    Citation: Journal of Cheminformatics 2022 14:22
  25. The introduction of machine learning to small molecule research– an inherently multidisciplinary field in which chemists and data scientists combine their expertise and collaborate - has been vital to making s...

    Authors: Christina Humer, Henry Heberle, Floriane Montanari, Thomas Wolf, Florian Huber, Ryan Henderson, Julian Heinrich and Marc Streit
    Citation: Journal of Cheminformatics 2022 14:21
  26. Chemical space exploration is a major task of the hit-finding process during the pursuit of novel chemical entities. Compared with other screening technologies, computational de novo design has become a popula...

    Authors: Chong Lu, Shien Liu, Weihua Shi, Jun Yu, Zhou Zhou, Xiaoxiao Zhang, Xiaoli Lu, Faji Cai, Ning Xia and Yikai Wang
    Citation: Journal of Cheminformatics 2022 14:19
  27. Molecular optimization aims to improve the drug profile of a starting molecule. It is a fundamental problem in drug discovery but challenging due to (i) the requirement of simultaneous optimization of multiple...

    Authors: Jiazhen He, Eva Nittinger, Christian Tyrchan, Werngard Czechtizky, Atanas Patronov, Esben Jannik Bjerrum and Ola Engkvist
    Citation: Journal of Cheminformatics 2022 14:18
  28. Structure-based drug repositioning has emerged as a promising alternative to conventional drug development. Regardless of the many success stories reported over the past years and the novel breakthroughs on th...

    Authors: Melissa F. Adasme, Sarah Naomi Bolz, Ali Al-Fatlawi and Michael Schroeder
    Citation: Journal of Cheminformatics 2022 14:17
  29. The Janus kinase (JAK) family plays a pivotal role in most cytokine-mediated inflammatory and autoimmune responses via JAK/STAT signaling, and administration of JAK inhibitors is a promising therapeutic strate...

    Authors: Yimeng Wang, Yaxin Gu, Chaofeng Lou, Yuning Gong, Zengrui Wu, Weihua Li, Yun Tang and Guixia Liu
    Citation: Journal of Cheminformatics 2022 14:16
  30. Drug-target binding affinity (DTA) reflects the strength of the drug-target interaction; therefore, predicting the DTA can considerably benefit drug discovery by narrowing the search space and pruning drug-tar...

    Authors: Junjie Wang, NaiFeng Wen, Chunyu Wang, Lingling Zhao and Liang Cheng
    Citation: Journal of Cheminformatics 2022 14:14
  31. Chemical–genetic interaction profiling is a genetic approach that quantifies the susceptibility of a set of mutants depleted in specific gene product(s) to a set of chemical compounds. With the recent advances...

    Authors: Chengyou Liu, Andrew M. Hogan, Hunter Sturm, Mohd Wasif Khan, Md. Mohaiminul Islam, A. S. M. Zisanur Rahman, Rebecca Davis, Silvia T. Cardona and Pingzhao Hu
    Citation: Journal of Cheminformatics 2022 14:12
  32. Graph based methods are increasingly important in chemistry and drug discovery, with applications ranging from QSAR to molecular generation. Combining graph neural networks and deep metric learning concepts, w...

    Authors: Damien E. Coupry and Peter Pogány
    Citation: Journal of Cheminformatics 2022 14:11
  33. Deep learning’s automatic feature extraction has been a revolutionary addition to computational drug discovery, infusing both the capabilities of learning abstract features and discovering complex molecular pa...

    Authors: Arash Keshavarzi Arshadi, Milad Salem, Arash Firouzbakht and Jiann Shiun Yuan
    Citation: Journal of Cheminformatics 2022 14:10
  34. A key concept in drug design is how natural variants, especially the ones occurring in the binding site of drug targets, affect the inter-individual drug response and efficacy by altering binding affinity. The...

    Authors: Ammar Ammar, Rachel Cavill, Chris Evelo and Egon Willighagen
    Citation: Journal of Cheminformatics 2022 14:8
  35. In this work we explore the properties which make many real-life global optimization problems extremely difficult to handle, and some of the common techniques used in literature to address them. We then introd...

    Authors: Michael Freitas Gustavo and Toon Verstraelen
    Citation: Journal of Cheminformatics 2022 14:7
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