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  1. We developed ChemScanner, a software that can be used for the extraction of chemical information from ChemDraw binary (CDX) or ChemDraw XML-based (CDXML) files and to retrieve the ChemDraw scheme from DOC, DOCX o...

    Authors: An Nguyen, Yu-Chieh Huang, Pierre Tremouilhac, Nicole Jung and Stefan Bräse

    Citation: Journal of Cheminformatics 2019 11:77

    Content type: Software

    Published on:

  2. The chemfp project has had four main goals: (1) promote the FPS format as a text-based exchange format for dense binary cheminformatics fingerprints, (2) develop a high-performance implementation of the BitBou...

    Authors: Andrew Dalke

    Citation: Journal of Cheminformatics 2019 11:76

    Content type: Methodology

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  3. Metabolic profiling has been shown to be useful to improve our understanding of complex metabolic processes. Shared data are key to the analysis and validation of metabolic profiling and untargeted spectral an...

    Authors: Julien Wist

    Citation: Journal of Cheminformatics 2019 11:75

    Content type: Research article

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  4. Deep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture, LatentGAN, which combines an autoencoder and a generativ...

    Authors: Oleksii Prykhodko, Simon Viet Johansson, Panagiotis-Christos Kotsias, Josep Arús-Pous, Esben Jannik Bjerrum, Ola Engkvist and Hongming Chen

    Citation: Journal of Cheminformatics 2019 11:74

    Content type: Research article

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  5. Drug repurposing offers a promising alternative to dramatically shorten the process of traditional de novo development of a drug. These efforts leverage the fact that a single molecule can act on multiple targ...

    Authors: Fan Wang, Feng-Xu Wu, Cheng-Zhang Li, Chen-Yang Jia, Sun-Wen Su, Ge-Fei Hao and Guang-Fu Yang

    Citation: Journal of Cheminformatics 2019 11:73

    Content type: Research article

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  6. Recurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures. He...

    Authors: Josep Arús-Pous, Simon Viet Johansson, Oleksii Prykhodko, Esben Jannik Bjerrum, Christian Tyrchan, Jean-Louis Reymond, Hongming Chen and Ola Engkvist

    Citation: Journal of Cheminformatics 2019 11:71

    Content type: Research article

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  7. With the advancements in deep learning, deep generative models combined with graph neural networks have been successfully employed for data-driven molecular graph generation. Early methods based on the non-aut...

    Authors: Youngchun Kwon, Jiho Yoo, Youn-Suk Choi, Won-Joon Son, Dongseon Lee and Seokho Kang

    Citation: Journal of Cheminformatics 2019 11:70

    Content type: Research article

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  8. The QM9 dataset has become the golden standard for Machine Learning (ML) predictions of various chemical properties. QM9 is based on the GDB, which is a combinatorial exploration of the chemical space. ML mole...

    Authors: Marta Glavatskikh, Jules Leguy, Gilles Hunault, Thomas Cauchy and Benoit Da Mota

    Citation: Journal of Cheminformatics 2019 11:69

    Content type: Research article

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  9. The goal of quantitative structure activity relationship (QSAR) learning is to learn a function that, given the structure of a small molecule (a potential drug), outputs the predicted activity of the compound....

    Authors: Noureddin Sadawi, Ivan Olier, Joaquin Vanschoren, Jan N. van Rijn, Jeremy Besnard, Richard Bickerton, Crina Grosan, Larisa Soldatova and Ross D. King

    Citation: Journal of Cheminformatics 2019 11:68

    Content type: Research article

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  10. Molecular descriptor (2D) and three dimensional (3D) shape based similarity methods are widely used in ligand based virtual drug design. In the present study pairwise structure comparisons among a set of 4858 ...

    Authors: Anna Lovrics, Veronika F. S. Pape, Dániel Szisz, Adrián Kalászi, Petra Heffeter, Csaba Magyar and Gergely Szakács

    Citation: Journal of Cheminformatics 2019 11:67

    Content type: Research article

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  11. Drugs have become an essential part of our lives due to their ability to improve people’s health and quality of life. However, for many diseases, approved drugs are not yet available or existing drugs have und...

    Authors: David Ruano-Ordás, Lindsey Burggraaff, Rongfang Liu, Cas van der Horst, Laura H. Heitman, Michael T. M. Emmerich, Jose R. Mendez, Iryna Yevseyeva and Gerard J. P. van Westen

    Citation: Journal of Cheminformatics 2019 11:66

    Content type: Research article

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  12. Recently Bosc et al. (J Cheminform 11(1): 4, 2019), published an article describing a case study that directly compares conformal predictions with traditional QSAR methods for large-scale predictions of target...

    Authors: Damjan Krstajic

    Citation: Journal of Cheminformatics 2019 11:65

    Content type: Letter to the Editor

    Published on:

    The original article was published in Journal of Cheminformatics 2019 11:4

    The Letter to the Editor to this article has been published in Journal of Cheminformatics 2019 11:64

  13. In response to Krstajic’s letter to the editor concerning our published paper, we here take the opportunity to reply, to re-iterate that no errors in our work were identified, to provide further details, and t...

    Authors: Nicolas Bosc, Francis Atkinson, Eloy Félix, Anna Gaulton, Anne Hersey and Andrew R. Leach

    Citation: Journal of Cheminformatics 2019 11:64

    Content type: Letter to the Editor

    Published on:

    The original article was published in Journal of Cheminformatics 2019 11:65

    The Research article to this article has been published in Journal of Cheminformatics 2019 11:4

  14. Currently, the submission guidelines for the Journal of Cheminformatics say it will “only publish research or software that is entirely reproducible by third parties.” They go on to specify that being reproduc...

    Authors: Robert D. Clark

    Citation: Journal of Cheminformatics 2019 11:62

    Content type: Commentary

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  15. Scaffold analysis of compound data sets has reemerged as a chemically interpretable alternative to machine learning for chemical space and structure–activity relationships analysis. In this context, analog ser...

    Authors: J. Jesús Naveja, B. Angélica Pilón-Jiménez, Jürgen Bajorath and José L. Medina-Franco

    Citation: Journal of Cheminformatics 2019 11:61

    Content type: Methodology

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  16. The logarithmic acid dissociation constant pKa reflects the ionization of a chemical, which affects lipophilicity, solubility, protein binding, and ability to pass through the plasma membrane. Thus, pKa affect...

    Authors: Kamel Mansouri, Neal F. Cariello, Alexandru Korotcov, Valery Tkachenko, Chris M. Grulke, Catherine S. Sprankle, David Allen, Warren M. Casey, Nicole C. Kleinstreuer and Antony J. Williams

    Citation: Journal of Cheminformatics 2019 11:60

    Content type: Research article

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  17. We present machine learning (ML) models for hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD) strengths. Quantum chemical (QC) free energies in solution for 1:1 hydrogen-bonded complex formation to th...

    Authors: Christoph A. Bauer, Gisbert Schneider and Andreas H. Göller

    Citation: Journal of Cheminformatics 2019 11:59

    Content type: Research article

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  18. The median lethal dose for rodent oral acute toxicity (LD50) is a standard piece of information required to categorize chemicals in terms of the potential hazard posed to human health after acute exposure. The...

    Authors: Domenico Gadaleta, Kristijan Vuković, Cosimo Toma, Giovanna J. Lavado, Agnes L. Karmaus, Kamel Mansouri, Nicole C. Kleinstreuer, Emilio Benfenati and Alessandra Roncaglioni

    Citation: Journal of Cheminformatics 2019 11:58

    Content type: Research article

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  19. PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to th...

    Authors: Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Jian Zhang, Asta Gindulyte and Evan E. Bolton

    Citation: Journal of Cheminformatics 2019 11:56

    Content type: Database

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  20. This study aims at improving upon existing activity predictions methods by augmenting chemical structure fingerprints with bio-activity based fingerprints derived from high-throughput screening (HTS) data (HTS...

    Authors: Oliver Laufkötter, Noé Sturm, Jürgen Bajorath, Hongming Chen and Ola Engkvist

    Citation: Journal of Cheminformatics 2019 11:54

    Content type: Research article

    Published on:

  21. Performance of structure-based molecular docking largely depends on the accuracy of scoring functions. One important type of scoring functions are knowledge-based potentials derived from known three-dimensiona...

    Authors: Pin Chen, Yaobin Ke, Yutong Lu, Yunfei Du, Jiahui Li, Hui Yan, Huiying Zhao, Yaoqi Zhou and Yuedong Yang

    Citation: Journal of Cheminformatics 2019 11:52

    Content type: Research article

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  22. Bulk water molecular dynamics simulations based on a series of atomistic water potentials (TIP3P, TIP4P/Ew, SPC/E and OPC) are compared using new techniques from the field of topological data analysis. The top...

    Authors: Lee Steinberg, John Russo and Jeremy Frey

    Citation: Journal of Cheminformatics 2019 11:48

    Content type: Research article

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    The Correction to this article has been published in Journal of Cheminformatics 2019 11:51

  23. To better leverage the accumulated bioactivity data in the ChEMBL database, we have developed Bioactivity-explorer, a web application for interactive visualization and exploration of the large-scale bioactivit...

    Authors: Lu Liang, Chunfeng Ma, Tengfei Du, Yufei Zhao, Xiaoyong Zhao, Mengmeng Liu, Zhonghua Wang and Jianping Lin

    Citation: Journal of Cheminformatics 2019 11:47

    Content type: Software

    Published on:

  24. Analysis of compound–protein interactions (CPIs) has become a crucial prerequisite for drug discovery and drug repositioning. In vitro experiments are commonly used in identifying CPIs, but it is not feasible ...

    Authors: Munhwan Lee, Hyeyeon Kim, Hyunwhan Joe and Hong-Gee Kim

    Citation: Journal of Cheminformatics 2019 11:46

    Content type: Research article

    Published on:

  25. The existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields ranging from drug design to metabolomics. Transparent search acro...

    Authors: Miroslav Kratochvíl, Jiří Vondrášek and Jakub Galgonek

    Citation: Journal of Cheminformatics 2019 11:45

    Content type: Software

    Published on:

  26. Developing predictive and transparent approaches to the analysis of metabolite profiles across patient cohorts is of critical importance for understanding the events that trigger or modulate traits of interest...

    Authors: Jeremy R. Ash, Melaine A. Kuenemann, Daniel Rotroff, Alison Motsinger-Reif and Denis Fourches

    Citation: Journal of Cheminformatics 2019 11:43

    Content type: Research article

    Published on:

  27. Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such ta...

    Authors: Martin Pérez-Pérez, Gael Pérez-Rodríguez, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger and Anália Lourenço

    Citation: Journal of Cheminformatics 2019 11:42

    Content type: Research article

    Published on:

  28. The application of convolutional neural networks (ConvNets) to harness high-content screening images or 2D compound representations is gaining increasing attention in drug discovery. However, existing applicat...

    Authors: Isidro Cortés-Ciriano and Andreas Bender

    Citation: Journal of Cheminformatics 2019 11:41

    Content type: Research article

    Published on:

  29. Traditional quantitative structure-activity relationship models usually neglect the molecular alterations happening in the exposed systems (the mechanism of action, MOA), that mediate between structural proper...

    Authors: Angela Serra, Serli Önlü, Pietro Coretto and Dario Greco

    Citation: Journal of Cheminformatics 2019 11:38

    Content type: Research article

    Published on:

  30. The Ertl algorithm for automated functional groups (FG) detection and extraction of organic molecules is implemented on the basis of the Chemistry Development Kit (CDK). A distinct impact of the chosen CDK aro...

    Authors: Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck and Achim Zielesny

    Citation: Journal of Cheminformatics 2019 11:37

    Content type: Software

    Published on:

  31. Despite the increasing knowledge in both the chemical and biological domains the assimilation and exploration of heterogeneous datasets, encoding information about the chemical, bioactivity and phenotypic prop...

    Authors: Chad H. G. Allen, Lewis H. Mervin, Samar Y. Mahmoud and Andreas Bender

    Citation: Journal of Cheminformatics 2019 11:36

    Content type: Research article

    Published on:

  32. Over the last 5 years deep learning has progressed tremendously in both image recognition and natural language processing. Now it is increasingly applied to other data rich fields. In drug discovery, recurrent...

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

    Citation: Journal of Cheminformatics 2019 11:35

    Content type: Research article

    Published on:

  33. Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library pr...

    Authors: Patrick J. Ropp, Jacob O. Spiegel, Jennifer L. Walker, Harrison Green, Guillermo A. Morales, Katherine A. Milliken, John J. Ringe and Jacob D. Durrant

    Citation: Journal of Cheminformatics 2019 11:34

    Content type: Software

    Published on:

  34. We describe a file format that is designed to represent mixtures of compounds in a way that is fully machine readable. This Mixfile format is intended to fill the same role for substances that are composed of mul...

    Authors: Alex M. Clark, Leah R. McEwen, Peter Gedeck and Barry A. Bunin

    Citation: Journal of Cheminformatics 2019 11:33

    Content type: Research article

    Published on:

  35. Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generati...

    Authors: Lucian Chan, Geoffrey R. Hutchison and Garrett M. Morris

    Citation: Journal of Cheminformatics 2019 11:32

    Content type: Research article

    Published on:

  36. It was highlighted that the original article [1] contained an error in the Funding section. This Correction article states the correct and incorrect versions of the Funding section.

    Authors: Domenico Gadaleta, Anna Lombardo, Cosimo Toma and Emilio Benfenati

    Citation: Journal of Cheminformatics 2019 11:31

    Content type: Correction

    Published on:

    The original article was published in Journal of Cheminformatics 2018 10:60

  37. Covalent DNA modifications, such as 5-methylcytosine (5mC), are increasingly the focus of numerous research programs. In eukaryotes, both 5mC and 5-hydroxymethylcytosine (5hmC) are now recognized as stable epi...

    Authors: Ankur Jai Sood, Coby Viner and Michael M. Hoffman

    Citation: Journal of Cheminformatics 2019 11:30

    Content type: Database

    Published on:

  38. Owing to the increase in freely available software and data for cheminformatics and structural bioinformatics, research for computer-aided drug design (CADD) is more and more built on modular, reproducible, an...

    Authors: Dominique Sydow, Andrea Morger, Maximilian Driller and Andrea Volkamer

    Citation: Journal of Cheminformatics 2019 11:29

    Content type: Software

    Published on:

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