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  1. The quality of data used for QSAR model derivation is extremely important as it strongly affects the final robustness and predictive power of the model. Ambiguous or wrong structures need to be carefully check...

    Authors: Domenico Gadaleta, Anna Lombardo, Cosimo Toma and Emilio Benfenati
    Citation: Journal of Cheminformatics 2018 10:60
    Content type: Research article Published on:

    The Correction to this article has been published in Journal of Cheminformatics 2019 11:31

  4. The goal of chemmodlab is to streamline the fitting and assessment pipeline for many machine learning models in R, making it easy for researchers to compare the utility of these models. While focused on implem...

    Authors: Jeremy R. Ash and Jacqueline M. Hughes-Oliver
    Citation: Journal of Cheminformatics 2018 10:57
    Content type: Software Published on:

  5. Current ligand-based machine learning methods in virtual screening rely heavily on molecular fingerprinting for preprocessing, i.e., explicit description of ligands’ structural and physicochemical properties i...

    Authors: Raghuram Srinivas, Pavel V. Klimovich and Eric C. Larson
    Citation: Journal of Cheminformatics 2018 10:56
    Content type: Research article Published on:

  6. Simplified representation of compound databases has several applications in cheminformatics. Herein, we introduce an alternative and general method to build single fingerprint representations of compound datab...

    Authors: Norberto Sánchez-Cruz and José L. Medina-Franco
    Citation: Journal of Cheminformatics 2018 10:55
    Content type: Methodology Published on:

  7. Topological data analysis is a family of recent mathematical techniques seeking to understand the ‘shape’ of data, and has been used to understand the structure of the descriptor space produced from a standard...

    Authors: Mariam Pirashvili, Lee Steinberg, Francisco Belchi Guillamon, Mahesan Niranjan, Jeremy G. Frey and Jacek Brodzki
    Citation: Journal of Cheminformatics 2018 10:54
    Content type: Research article Published on:

  9. When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typicall...

    Authors: Yasemin Yesiltepe, Jamie R. Nuñez, Sean M. Colby, Dennis G. Thomas, Mark I. Borkum, Patrick N. Reardon, Nancy M. Washton, Thomas O. Metz, Justin G. Teeguarden, Niranjan Govind and Ryan S. Renslow
    Citation: Journal of Cheminformatics 2018 10:52
    Content type: Research article Published on:

  10. Several topological (2D) and geometric (3D) molecular descriptors (MDs) are calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation process. To this end, norm-, mean- and statis...

    Authors: César R. García-Jacas, Lisset Cabrera-Leyva, Yovani Marrero-Ponce, José Suárez-Lezcano, Fernando Cortés-Guzmán, Mario Pupo-Meriño and Ricardo Vivas-Reyes
    Citation: Journal of Cheminformatics 2018 10:51
    Content type: Research article Published on:

  11. Fast and accurate identification of potential drug candidates against therapeutic targets (i.e., drug–target interactions, DTIs) is a fundamental step in the early drug discovery process. However, experimental...

    Authors: Ming Hao, Stephen H. Bryant and Yanli Wang
    Citation: Journal of Cheminformatics 2018 10:50
    Content type: Research article Published on:

  12. Ligand-based predictive modeling is widely used to generate predictive models aiding decision making in e.g. drug discovery projects. With growing data sets and requirements on low modeling time comes the nece...

    Authors: Alexander Kensert, Jonathan Alvarsson, Ulf Norinder and Ola Spjuth
    Citation: Journal of Cheminformatics 2018 10:49
    Content type: Research article Published on:

  14. Quantitative structure-activity relationship (QSAR) models are important tools used in discovering new drug candidates and identifying potentially harmful environmental chemicals. These models often face two f...

    Authors: Ilya A. Balabin and Richard S. Judson
    Citation: Journal of Cheminformatics 2018 10:47
    Content type: Research article Published on:

  16. Chemical database searching has become a fixture in many non-targeted identification workflows based on high-resolution mass spectrometry (HRMS). However, the form of a chemical structure observed in HRMS does...

    Authors: Andrew D. McEachran, Kamel Mansouri, Chris Grulke, Emma L. Schymanski, Christoph Ruttkies and Antony J. Williams
    Citation: Journal of Cheminformatics 2018 10:45
    Content type: Methodology Published on:

    The Data Descriptor to this article has been published in Scientific Data 2019 6:141

  17. Predicting the equilibrium solubility of organic, crystalline materials at all relevant temperatures is crucial to the digital design of manufacturing unit operations in the chemical industries. The work repor...

    Authors: Richard L. Marchese Robinson, Kevin J. Roberts and Elaine B. Martin
    Citation: Journal of Cheminformatics 2018 10:44
    Content type: Research article Published on:

  19. Ambit-SMIRKS is an open source software, enabling structure transformation via the SMIRKS language and implemented as an extension of Ambit-SMARTS. As part of the Ambit project it builds on top of The Chemistr...

    Authors: Nikolay Kochev, Svetlana Avramova and Nina Jeliazkova
    Citation: Journal of Cheminformatics 2018 10:42
    Content type: Software Published on:

  20. Modern phenotypic high-throughput screens (HTS) present several challenges including identifying the target(s) that mediate the effect seen in the screen, characterizing ‘hits’ with a polypharmacologic target ...

    Authors: Robert J. Allaway, Salvatore La Rosa, Justin Guinney and Sara J. C. Gosline
    Citation: Journal of Cheminformatics 2018 10:41
    Content type: Software Published on:

  21. Betulin derivatives have been proven effective in vitro against Leishmania donovani amastigotes, which cause visceral leishmaniasis. Identifying the molecular targets and molecular mechanisms underlying their act...

    Authors: Yuezhou Zhang, Henri Xhaard and Leo Ghemtio
    Citation: Journal of Cheminformatics 2018 10:40
    Content type: Research article Published on:

  23. The Ketcher editor, available as an Open Source software package for drawing chemical structures, has been expanded to include several features that allow storage, management and application of templates, as w...

    Authors: Serhii Kotov, Pierre Tremouilhac, Nicole Jung and Stefan Bräse
    Citation: Journal of Cheminformatics 2018 10:38
    Content type: Software Published on:

  24. Pharmacovigilance (PV) databases record the benefits and risks of different drugs, as a means to ensure their safe and effective use. Creating and maintaining such resources can be complex, since a particular ...

    Authors: Paul Thompson, Sophia Daikou, Kenju Ueno, Riza Batista-Navarro, Jun’ichi Tsujii and Sophia Ananiadou
    Citation: Journal of Cheminformatics 2018 10:37
    Content type: Research article Published on:

  25. PubChem is a chemical information repository, consisting of three primary databases: Substance, Compound, and BioAssay. When individual data contributors submit chemical substance descriptions to Substance, th...

    Authors: Volker D. Hähnke, Sunghwan Kim and Evan E. Bolton
    Citation: Journal of Cheminformatics 2018 10:36
    Content type: Research article Published on:

  26. Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims a...

    Authors: Karina van den Broek, Mirco Daniel, Matthias Epple, Hubert Kuhn, Jonas Schaub and Achim Zielesny
    Citation: Journal of Cheminformatics 2018 10:35
    Content type: Software Published on:

  27. Autophagy is an important homeostatic cellular recycling mechanism responsible for degrading unnecessary or dysfunctional cellular organelles and proteins in all living cells. In addition to its vital homeosta...

    Authors: Ning-Ning Wang, Jie Dong, Lin Zhang, Defang Ouyang, Yan Cheng, Alex F. Chen, Ai-Ping Lu and Dong-Sheng Cao
    Citation: Journal of Cheminformatics 2018 10:34
    Content type: Database Published on:

  29. Epigenetic therapies are being investigated for the treatment of cancer, cognitive disorders, metabolic alterations and autoinmune diseases. Among the different epigenetic target families, protein lysine methy...

    Authors: Obdulia Rabal, Andrea Castellar and Julen Oyarzabal
    Citation: Journal of Cheminformatics 2018 10:32
    Content type: Research article Published on:

  30. We propose a molecular generative model based on the conditional variational autoencoder for de novo molecular design. It is specialized to control multiple molecular properties simultaneously by imposing them...

    Authors: Jaechang Lim, Seongok Ryu, Jin Woo Kim and Woo Youn Kim
    Citation: Journal of Cheminformatics 2018 10:31
    Content type: Research article Published on:

  31. Recently, many biological experiments have indicated that microRNAs (miRNAs) are a newly discovered small molecule (SM) drug targets that play an important role in the development and progression of human comp...

    Authors: Jia Qu, Xing Chen, Ya-Zhou Sun, Jian-Qiang Li and Zhong Ming
    Citation: Journal of Cheminformatics 2018 10:30
    Content type: Research article Published on:

  32. Current pharmaceutical research and development (R&D) is a high-risk investment which is usually faced with some unexpected even disastrous failures in different stages of drug discovery. One main reason for R...

    Authors: Jie Dong, Ning-Ning Wang, Zhi-Jiang Yao, Lin Zhang, Yan Cheng, Defang Ouyang, Ai-Ping Lu and Dong-Sheng Cao
    Citation: Journal of Cheminformatics 2018 10:29
    Content type: Software Published on:

  33. Chemical named entity recognition (NER) is an active field of research in biomedical natural language processing. To facilitate the development of new and superior chemical NER systems, BioCreative released th...

    Authors: Ilia Korvigo, Maxim Holmatov, Anatolii Zaikovskii and Mikhail Skoblov
    Citation: Journal of Cheminformatics 2018 10:28
    Content type: Software Published on:

  35. There has been a growing interest in multitask prediction in chemoinformatics, helped by the increasing use of deep neural networks in this field. This technique is applied to multitarget data sets, where comp...

    Authors: Antonio de la Vega de León, Beining Chen and Valerie J. Gillet
    Citation: Journal of Cheminformatics 2018 10:26
    Content type: Research article Published on:

  37. Tuberculosis (TB) is the world’s leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are ...

    Authors: Anurag Passi, Neeraj Kumar Rajput, David J. Wild and Anshu Bhardwaj
    Citation: Journal of Cheminformatics 2018 10:24
    Content type: Research article Published on:

  38. Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to des...

    Authors: Miguel Quirós, Saulius Gražulis, Saulė Girdzijauskaitė, Andrius Merkys and Antanas Vaitkus
    Citation: Journal of Cheminformatics 2018 10:23
    Content type: Research article Published on:

  39. The Reaction InChI (RInChI) extends the idea of the InChI, which provides a unique descriptor of molecular structures, towards reactions. Prototype versions of the RInChI have been available since 2011. The fi...

    Authors: Guenter Grethe, Gerd Blanke, Hans Kraut and Jonathan M. Goodman
    Citation: Journal of Cheminformatics 2018 10:22
    Content type: Research article Published on:

  40. Nuclear receptors (NR) are a class of proteins that are responsible for sensing steroid and thyroid hormones and certain other molecules. In that case, NR have the ability to regulate the expression of specifi...

    Authors: Tianyi Qiu, Dingfeng Wu, Jingxuan Qiu and Zhiwei Cao
    Citation: Journal of Cheminformatics 2018 10:21
    Content type: Research article Published on:

  42. In synthesis planning, the goal is to synthesize a target molecule from available starting materials, possibly optimizing costs such as price or environmental impact of the process. Current algorithmic approac...

    Authors: Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle and Peter F. Stadler
    Citation: Journal of Cheminformatics 2018 10:19
    Content type: Research Published on:

  43. Dye-sensitized solar cells (DSSCs) have garnered a lot of attention in recent years. The solar energy to power conversion efficiency of a DSSC is influenced by various components of the cell such as the dye, e...

    Authors: Vishwesh Venkatraman, Rajesh Raju, Solon P. Oikonomopoulos and Bjørn K. Alsberg
    Citation: Journal of Cheminformatics 2018 10:18
    Content type: Database Published on:

  44. Lipophilicity is a major determinant of ADMET properties and overall suitability of drug candidates. We have developed large-scale models to predict water–octanol distribution coefficient (logD) for chemical c...

    Authors: Maris Lapins, Staffan Arvidsson, Samuel Lampa, Arvid Berg, Wesley Schaal, Jonathan Alvarsson and Ola Spjuth
    Citation: Journal of Cheminformatics 2018 10:17
    Content type: Research article Published on:

  45. With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to b...

    Authors: Jie Dong, Zhi-Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Ai-Ping Lu, Alex F. Chen and Dong-Sheng Cao
    Citation: Journal of Cheminformatics 2018 10:16
    Content type: Software Published on:

  46. Protein ligand interaction fingerprints are a powerful approach for the analysis and assessment of docking poses to improve docking performance in virtual screening. In this study, a novel interaction fingerpr...

    Authors: Julia B. Jasper, Lina Humbeck, Tobias Brinkjost and Oliver Koch
    Citation: Journal of Cheminformatics 2018 10:15
    Content type: Research article Published on:

  49. A number of anti-retroviral drugs are being used for treating Human Immunodeficiency Virus (HIV) infection. Due to emergence of drug resistant strains, there is a constant quest to discover more effective anti...

    Authors: Abid Qureshi, Akanksha Rajput, Gazaldeep Kaur and Manoj Kumar
    Citation: Journal of Cheminformatics 2018 10:12
    Content type: Research article Published on:

  50. Both the automated generation of reaction networks and the automated prediction of synthetic trees require, in one way or another, the definition of possible transformations a molecule can undergo. One way of ...

    Authors: Pieter P. Plehiers, Guy B. Marin, Christian V. Stevens and Kevin M. Van Geem
    Citation: Journal of Cheminformatics 2018 10:11
    Content type: Research article Published on:
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