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  1. A key challenge in the field of Quantitative Structure Activity Relationships (QSAR) is how to effectively treat experimental error in the training and evaluation of computational models. It is often assumed i...

    Authors: Scott S. Kolmar and Christopher M. Grulke

    Citation: Journal of Cheminformatics 2021 13:92

    Content type: Research article

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  2. With the development of advanced technologies in cell-based phenotypic screening, phenotypic drug discovery (PDD) strategies have re-emerged as promising approaches in the identification and development of nov...

    Authors: Bryan Dafniet, Natacha Cerisier, Batiste Boezio, Anaelle Clary, Pierre Ducrot, Thierry Dorval, Arnaud Gohier, David Brown, Karine Audouze and Olivier Taboureau

    Citation: Journal of Cheminformatics 2021 13:91

    Content type: Research article

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  3. Rationalizing the identification of hidden similarities across the repertoire of druggable protein cavities remains a major hurdle to a true proteome-wide structure-based discovery of novel drug candidates. We...

    Authors: Merveille Eguida and Didier Rognan

    Citation: Journal of Cheminformatics 2021 13:90

    Content type: Research article

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  4. Recently, we have released the de novo design platform REINVENT in version 2.0. This improved and extended iteration supports far more features and scoring function components, which allows bespoke and tailor-...

    Authors: Jeff Guo, Jon Paul Janet, Matthias R. Bauer, Eva Nittinger, Kathryn A. Giblin, Kostas Papadopoulos, Alexey Voronov, Atanas Patronov, Ola Engkvist and Christian Margreitter

    Citation: Journal of Cheminformatics 2021 13:89

    Content type: Research article

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  5. In recent years, in silico molecular design is regaining interest. To generate on a computer molecules with optimized properties, scoring functions can be coupled with a molecular generator to design novel molecu...

    Authors: Francois Berenger and Koji Tsuda

    Citation: Journal of Cheminformatics 2021 13:88

    Content type: Research article

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  6. Scaffold hopping is a central task of modern medicinal chemistry for rational drug design, which aims to design molecules of novel scaffolds sharing similar target biological activities toward known hit molecu...

    Authors: Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng and Yuedong Yang

    Citation: Journal of Cheminformatics 2021 13:87

    Content type: Research article

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  7. In the process of drug discovery, the optimization of lead compounds has always been a challenge faced by pharmaceutical chemists. Matched molecular pair analysis (MMPA), a promising tool to efficiently extrac...

    Authors: Zi-Yi Yang, Li Fu, Ai-Ping Lu, Shao Liu, Ting-Jun Hou and Dong-Sheng Cao

    Citation: Journal of Cheminformatics 2021 13:86

    Content type: Research article

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  8. In polypharmacology drugs are required to bind to multiple specific targets, for example to enhance efficacy or to reduce resistance formation. Although deep learning has achieved a breakthrough in de novo des...

    Authors: Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman and Gerard J. P. van Westen

    Citation: Journal of Cheminformatics 2021 13:85

    Content type: Research article

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  9. Mass spectrometry data is one of the key sources of information in many workflows in medicine and across the life sciences. Mass fragmentation spectra are generally considered to be characteristic signatures o...

    Authors: Florian Huber, Sven van der Burg, Justin J. J. van der Hooft and Lars Ridder

    Citation: Journal of Cheminformatics 2021 13:84

    Content type: Methodology

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  10. The intelligent choice of extractants and entrainers can improve current mixture separation techniques allowing better efficiency and sustainability of chemical processes that are both used in industry and lab...

    Authors: Kyrylo Klimenko and Gonçalo V. S. M. Carrera

    Citation: Journal of Cheminformatics 2021 13:83

    Content type: Research article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Research article

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Software

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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

  32. 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

    Published on:

  33. 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

  34. 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

    Published on:

  35. 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

    Published on:

  36. 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

    Published on:

  37. 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

  38. 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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  39. 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

    Published on:

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