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  1. Natural products (NPs) represent one of the most important resources for discovering new drugs. Here we asked whether NP origin can be assigned from their molecular structure in a subset of 60,171 NPs in the r...

    Authors: Alice Capecchi and Jean-Louis Reymond
    Citation: Journal of Cheminformatics 2021 13:82
  2. Structure-based drug design depends on the detailed knowledge of the three-dimensional (3D) structures of protein–ligand binding complexes, but accurate prediction of ligand-binding poses is still a major chal...

    Authors: Chao Shen, Xueping Hu, Junbo Gao, Xujun Zhang, Haiyang Zhong, Zhe Wang, Lei Xu, Yu Kang, Dongsheng Cao and Tingjun Hou
    Citation: Journal of Cheminformatics 2021 13:81
  3. We present a sequence-to-sequence machine learning model for predicting the IUPAC name of a chemical from its standard International Chemical Identifier (InChI). The model uses two stacks of transformers in an...

    Authors: Jennifer Handsel, Brian Matthews, Nicola J. Knight and Simon J. Coles
    Citation: Journal of Cheminformatics 2021 13:79
  4. Non-target screening consists in searching a sample for all present substances, suspected or unknown, with very little prior knowledge about the sample. This approach has been introduced more than a decade ago...

    Authors: Myriam Guillevic, Aurore Guillevic, Martin K. Vollmer, Paul Schlauri, Matthias Hill, Lukas Emmenegger and Stefan Reimann
    Citation: Journal of Cheminformatics 2021 13:78
  5. Chemical diversity is one of the key term when dealing with machine learning and molecular generation. This is particularly true for quantum chemical datasets. The composition of which should be done meticulou...

    Authors: Jules Leguy, Marta Glavatskikh, Thomas Cauchy and Benoit Da Mota
    Citation: Journal of Cheminformatics 2021 13:76
  6. Many contemporary cheminformatics methods, including computer-aided de novo drug design, hold promise to significantly accelerate and reduce the cost of drug discovery. Thanks to this attractive outlook, the f...

    Authors: M. Sicho, X. Liu, D. Svozil and G. J. P. van Westen
    Citation: Journal of Cheminformatics 2021 13:73
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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

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

  22. 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
  23. 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

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

  24. 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
  25. 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
  26. 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
  27. 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

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

  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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