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  1. Drug–target interaction (DTI) prediction is a crucial step in drug discovery and repositioning as it reduces experimental validation costs if done right. Thus, developing in-silico methods to predict potential DT...

    Authors: Maha A. Thafar, Rawan S. Olayan, Somayah Albaradei, Vladimir B. Bajic, Takashi Gojobori, Magbubah Essack and Xin Gao

    Citation: Journal of Cheminformatics 2021 13:71

    Content type: Research article

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  2. Reliable uncertainty quantification for statistical models is crucial in various downstream applications, especially for drug design and discovery where mistakes may incur a large amount of cost. This topic ha...

    Authors: Dingyan Wang, Jie Yu, Lifan Chen, Xutong Li, Hualiang Jiang, Kaixian Chen, Mingyue Zheng and Xiaomin Luo

    Citation: Journal of Cheminformatics 2021 13:69

    Content type: Research article

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  3. Natural products from traditional medicine inherit bioactivity from their source herbs. However, the pharmacological mechanism of natural products is often unclear and studied insufficiently. Pathway fingerpri...

    Authors: Feifei Guo, Chunhong Jiang, Yujie Xi, Dan Wang, Yi Zhang, Ning Xie, Yi Guan, Fangbo Zhang and Hongjun Yang

    Citation: Journal of Cheminformatics 2021 13:68

    Content type: Research article

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  4. Improving the accuracy of absolute energies associated with rovibronic quantum states of molecules requires accurate high-resolution spectroscopy measurements. Such experiments yield transition wavenumbers fro...

    Authors: Péter Árendás, Tibor Furtenbacher and Attila G. Császár

    Citation: Journal of Cheminformatics 2021 13:67

    Content type: Research article

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  5. Depicting a ligand-receptor complex via Interaction Fingerprints has been shown to be both a viable data visualization and an analysis tool. The spectrum of its applications ranges from simple visualization of...

    Authors: Stefan Mordalski, Agnieszka Wojtuch, Igor Podolak, Rafał Kurczab and Andrzej J. Bojarski

    Citation: Journal of Cheminformatics 2021 13:66

    Content type: Software

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  6. We report the major conclusions of the online open-access workshop “Computational Applications in Secondary Metabolite Discovery (CAiSMD)” that took place from 08 to 10 March 2021. Invited speakers from academ...

    Authors: Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou-Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul Zierep, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Smith B. Babiaka, Romuald Tematio Fouedjou, Donatus B. Eni…

    Citation: Journal of Cheminformatics 2021 13:64

    Content type: Meeting report

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  7. The prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental sciences, drug discovery, and (eco)toxicology. Several systems predict single transformation...

    Authors: Jason Y. C. Tam, Tim Lorsbach, Sebastian Schmidt and Jörg S. Wicker

    Citation: Journal of Cheminformatics 2021 13:63

    Content type: Research article

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  8. Measurements of protein–ligand interactions have reproducibility limits due to experimental errors. Any model based on such assays will consequentially have such unavoidable errors influencing their performanc...

    Authors: Lewis H. Mervin, Maria-Anna Trapotsi, Avid M. Afzal, Ian P. Barrett, Andreas Bender and Ola Engkvist

    Citation: Journal of Cheminformatics 2021 13:62

    Content type: Research article

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  9. Ether-a-go-go-related gene (hERG) channel blockade by small molecules is a big concern during drug development in the pharmaceutical industry. Blockade of hERG channels may cause prolonged QT intervals that po...

    Authors: Abdul Karim, Matthew Lee, Thomas Balle and Abdul Sattar

    Citation: Journal of Cheminformatics 2021 13:60

    Content type: Research article

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  10. Scoring functions for the prediction of protein-ligand binding affinity have seen renewed interest in recent years when novel machine learning and deep learning methods started to consistently outperform class...

    Authors: Rocco Meli, Andrew Anighoro, Mike J. Bodkin, Garrett M. Morris and Philip C. Biggin

    Citation: Journal of Cheminformatics 2021 13:59

    Content type: Research article

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  11. Traditional techniques to identify macromolecular targets for drugs utilize solely the information on a query drug and a putative target. Nonetheless, the mechanisms of action of many drugs depend not only on...

    Authors: Guannan Liu, Manali Singha, Limeng Pu, Prasanga Neupane, Joseph Feinstein, Hsiao-Chun Wu, J. Ramanujam and Michal Brylinski

    Citation: Journal of Cheminformatics 2021 13:58

    Content type: Methodology

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  12. In this study we compare the three algorithms for the generation of conformer ensembles Biovia BEST, Schrödinger Prime macrocycle sampling (PMM) and Conformator (CONF) form the University of Hamburg, with ense...

    Authors: Lea Seep, Anne Bonin, Katharina Meier, Holger Diedam and Andreas H. Göller

    Citation: Journal of Cheminformatics 2021 13:55

    Content type: Research article

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  13. The scaffold representation is widely employed to classify bioactive compounds on the basis of common core structures or correlate compound classes with specific biological activities. In this paper, we presen...

    Authors: Candida Manelfi, Marica Gemei, Carmine Talarico, Carmen Cerchia, Anna Fava, Filippo Lunghini and Andrea Rosario Beccari

    Citation: Journal of Cheminformatics 2021 13:54

    Content type: Research article

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  14. The charged aerosol detector (CAD) is the latest representative of aerosol-based detectors that generate a response independent of the analytes’ chemical structure. This study was aimed at accurately predictin...

    Authors: Ruben Pawellek, Jovana Krmar, Adrian Leistner, Nevena Djajić, Biljana Otašević, Ana Protić and Ulrike Holzgrabe

    Citation: Journal of Cheminformatics 2021 13:53

    Content type: Research article

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  15. A Correction to this paper has been published: https://​doi.​org/​10.​1186/​s13321-021-00528-w

    Authors: Ondřej Schindler, Tomáš Raček, Aleksandra Maršavelski, Jaroslav Koča, Karel Berka and Radka Svobodová

    Citation: Journal of Cheminformatics 2021 13:52

    Content type: Correction

    Published on:

    The original article was published in Journal of Cheminformatics 2021 13:45

  16. Nonribosomal peptides and polyketides are natural products commonly synthesized by microorganisms. They are widely used in medicine, agriculture, environmental protection, and other fields. The structures of n...

    Authors: Jan Přívratský and Jiří Novák

    Citation: Journal of Cheminformatics 2021 13:51

    Content type: Software

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  17. The ability to access chemical information openly is an essential part of many scientific disciplines. The Journal of Cheminformatics is leading the way for rigorous, open cheminformatics in many ways, but the...

    Authors: Emma L. Schymanski and Evan E. Bolton

    Citation: Journal of Cheminformatics 2021 13:50

    Content type: Letter to the Editor

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    The Letter Response to this article has been published in Journal of Cheminformatics 2021 13:49

  18. The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generat...

    Authors: Mehmet Aziz Yirik, Maria Sorokina and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2021 13:48

    Content type: Software

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  19. Numerous ligand-based drug discovery projects are based on structure-activity relationship (SAR) analysis, such as Free-Wilson (FW) or matched molecular pair (MMP) analysis. Intrinsically they assume linearity...

    Authors: D. Gogishvili, E. Nittinger, C. Margreitter and C. Tyrchan

    Citation: Journal of Cheminformatics 2021 13:47

    Content type: Research article

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  20. Social media activity on a research article is considered to be an altmetric, a new measure to estimate research impact. Demonstrating software on Twitter is a powerful way to attract attention from a larger a...

    Authors: Naruki Yoshikawa, Ryuichi Kubo and Kazuki Z. Yamamoto

    Citation: Journal of Cheminformatics 2021 13:46

    Content type: Software

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  21. Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity ...

    Authors: Ondřej Schindler, Tomáš Raček, Aleksandra Maršavelski, Jaroslav Koča, Karel Berka and Radka Svobodová

    Citation: Journal of Cheminformatics 2021 13:45

    Content type: Research article

    Published on:

    The Correction to this article has been published in Journal of Cheminformatics 2021 13:52

  22. Target prediction is a crucial step in modern drug discovery. However, existing experimental approaches to target prediction are time-consuming and costly. Here, we introduce LigTMap, an online server with a f...

    Authors: Faraz Shaikh, Hio Kuan Tai, Nirali Desai and Shirley W. I. Siu

    Citation: Journal of Cheminformatics 2021 13:44

    Content type: Methodology

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  23. Molecular docking computationally predicts the conformation of a small molecule when binding to a receptor. Scoring functions are a vital piece of any molecular docking pipeline as they determine the fitness o...

    Authors: Andrew T. McNutt, Paul Francoeur, Rishal Aggarwal, Tomohide Masuda, Rocco Meli, Matthew Ragoza, Jocelyn Sunseri and David Ryan Koes

    Citation: Journal of Cheminformatics 2021 13:43

    Content type: Software

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  24. Interpretation of QSAR models is useful to understand the complex nature of biological or physicochemical processes, guide structural optimization or perform knowledge-based validation of QSAR models. Highly p...

    Authors: Mariia Matveieva and Pavel Polishchuk

    Citation: Journal of Cheminformatics 2021 13:41

    Content type: Research article

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  25. The software for the IUPAC Chemical Identifier, InChI, is extraordinarily reliable. It has been tested on large databases around the world, and has proved itself to be an essential tool in the handling and int...

    Authors: Jonathan M. Goodman, Igor Pletnev, Paul Thiessen, Evan Bolton and Stephen R. Heller

    Citation: Journal of Cheminformatics 2021 13:40

    Content type: Research article

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  26. Deep generative models have shown the ability to devise both valid and novel chemistry, which could significantly accelerate the identification of bioactive compounds. Many current models, however, use molecul...

    Authors: Morgan Thomas, Robert T. Smith, Noel M. O’Boyle, Chris de Graaf and Andreas Bender

    Citation: Journal of Cheminformatics 2021 13:39

    Content type: Research article

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  27. The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF ...

    Authors: Jakub Galgonek and Jiří Vondrášek

    Citation: Journal of Cheminformatics 2021 13:38

    Content type: Software

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  28. South African Natural Compounds Database (SANCDB; https://​sancdb.​rubi.​ru.​ac.​za/​) is the sole and a fully referenced database of natural chemical compounds of...

    Authors: Bakary N’tji Diallo, Michael Glenister, Thommas M. Musyoka, Kevin Lobb and Özlem Tastan Bishop

    Citation: Journal of Cheminformatics 2021 13:37

    Content type: Research article

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  29. Virtual screening, which can computationally predict the presence or absence of protein–compound interactions, has attracted attention as a large-scale, low-cost, and short-term search method for seed compound...

    Authors: Narumi Watanabe, Yuuto Ohnuki and Yasubumi Sakakibara

    Citation: Journal of Cheminformatics 2021 13:36

    Content type: Research article

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  30. Machine learning methods are widely used in drug discovery and toxicity prediction. While showing overall good performance in cross-validation studies, their predictive power (often) drops in cases where the q...

    Authors: Andrea Morger, Fredrik Svensson, Staffan Arvidsson McShane, Niharika Gauraha, Ulf Norinder, Ola Spjuth and Andrea Volkamer

    Citation: Journal of Cheminformatics 2021 13:35

    Content type: Research article

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  31. Chemical compounds can be identified through a graphical depiction, a suitable string representation, or a chemical name. A universally accepted naming scheme for chemistry was established by the International...

    Authors: Kohulan Rajan, Achim Zielesny and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2021 13:34

    Content type: Research article

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  32. Despite being a central concept in cheminformatics, molecular similarity has so far been limited to the simultaneous comparison of only two molecules at a time and using one index, generally the Tanimoto coeff...

    Authors: Ramón Alain Miranda-Quintana, Anita Rácz, Dávid Bajusz and Károly Héberger

    Citation: Journal of Cheminformatics 2021 13:33

    Content type: Research article

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  33. Quantification of the similarity of objects is a key concept in many areas of computational science. This includes cheminformatics, where molecular similarity is usually quantified based on binary fingerprints...

    Authors: Ramón Alain Miranda-Quintana, Dávid Bajusz, Anita Rácz and Károly Héberger

    Citation: Journal of Cheminformatics 2021 13:32

    Content type: Research article

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  34. This article describes Flame, an open source software for building predictive models and supporting their use in production environments. Flame is a web application with a web-based graphic interface, which ca...

    Authors: Manuel Pastor, José Carlos Gómez-Tamayo and Ferran Sanz

    Citation: Journal of Cheminformatics 2021 13:31

    Content type: Software

    Published on:

  35. The assessment of protein–ligand interactions is critical at early stage of drug discovery. Computational approaches for efficiently predicting such interactions facilitate drug development. Recently, methods ...

    Authors: Fan Hu, Jiaxin Jiang, Dongqi Wang, Muchun Zhu and Peng Yin

    Citation: Journal of Cheminformatics 2021 13:30

    Content type: Research article

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  36. Quantitative structure activity relationships (QSAR) modelling is a well-known computational tool, often used in a wide variety of applications. Yet one of the major drawbacks of conventional QSAR modelling is...

    Authors: Amit Kumar Halder and M. Natália Dias Soeiro Cordeiro

    Citation: Journal of Cheminformatics 2021 13:29

    Content type: Software

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  37. In drug discovery, rapid and accurate prediction of protein–ligand binding affinities is a pivotal task for lead optimization with acceptable on-target potency as well as pharmacological efficacy. Furthermore,...

    Authors: Surendra Kumar and Mi-hyun Kim

    Citation: Journal of Cheminformatics 2021 13:28

    Content type: Research article

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  38. A main challenge in drug discovery is finding molecules with a desirable balance of multiple properties. Here, we focus on the task of molecular optimization, where the goal is to optimize a given starting mol...

    Authors: Jiazhen He, Huifang You, Emil Sandström, Eva Nittinger, Esben Jannik Bjerrum, Christian Tyrchan, Werngard Czechtizky and Ola Engkvist

    Citation: Journal of Cheminformatics 2021 13:26

    Content type: Research article

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  39. The experimental values of skin permeability coefficients, required for dermal exposure assessment, are not readily available for many chemicals. The existing estimation approaches are either less accurate or ...

    Authors: Sana Naseem, Yasuyuki Zushi and Deedar Nabi

    Citation: Journal of Cheminformatics 2021 13:25

    Content type: Research article

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  40. Here, we introduce a new molecule optimization method, MolFinder, based on an efficient global optimization algorithm, the conformational space annealing algorithm, and the SMILES representation. MolFinder fin...

    Authors: Yongbeom Kwon and Juyong Lee

    Citation: Journal of Cheminformatics 2021 13:24

    Content type: Research article

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  41. Chemical data is increasingly openly available in databases such as PubChem, which contains approximately 110 million compound entries as of February 2021. With the availability of data at such scale, the burd...

    Authors: Janna Hastings, Martin Glauer, Adel Memariani, Fabian Neuhaus and Till Mossakowski

    Citation: Journal of Cheminformatics 2021 13:23

    Content type: Research article

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