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  1. Content type: Research article

    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

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  2. Content type: Software

    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

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  3. Content type: Research article

    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

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  4. Content type: Software

    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

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  5. Content type: Research article

    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

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  6. Content type: Research article

    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

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  7. Content type: Research article

    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

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  8. Content type: Research article

    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

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  9. Content type: Software

    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

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. Content type: Software

    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

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  13. Content type: Research article

    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

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  14. Content type: Research article

    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

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  15. Content type: Correction

    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

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

  16. Content type: Database

    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

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  17. Content type: Software

    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

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  18. Content type: Research article

    Because drug–drug interactions (DDIs) may cause adverse drug reactions or contribute to complex-disease treatments, it is important to identify DDIs before multiple-drug medications are prescribed. As the alte...

    Authors: Jian-Yu Shi, Kui-Tao Mao, Hui Yu and Siu-Ming Yiu

    Citation: Journal of Cheminformatics 2019 11:28

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  19. Content type: Methodology

    Several QSAR methodology developments have shown promise in recent years. These include the consensus approach to generate the final prediction of a model, utilizing new, advanced machine learning algorithms a...

    Authors: Kristijan Vukovic, Domenico Gadaleta and Emilio Benfenati

    Citation: Journal of Cheminformatics 2019 11:27

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  20. Content type: Research article

    The process of ligand binding to a biological target can be represented as the equilibrium between the relevant solvated and bound states of the ligand. This which is the basis of structure-based, rigorous met...

    Authors: Willem Jespers, Mauricio Esguerra, Johan Åqvist and Hugo Gutiérrez-de-Terán

    Citation: Journal of Cheminformatics 2019 11:26

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  21. Content type: Research article

    Random peptide libraries that cover large search spaces are often used for the discovery of new binders, even when the target is unknown. To ensure an accurate population representation, there is a tendency to...

    Authors: Daniela Kalafatovic, Goran Mauša, Toni Todorovski and Ernest Giralt

    Citation: Journal of Cheminformatics 2019 11:25

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  22. Content type: Research article

    Docking is commonly used in drug discovery to predict how ligand binds to protein target. Best programs are generally able to generate a correct solution, yet often fail to identify it. In the case of drug-lik...

    Authors: Célien Jacquemard, Malgorzata N. Drwal, Jérémy Desaphy and Esther Kellenberger

    Citation: Journal of Cheminformatics 2019 11:24

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  23. Content type: Research article

    Scientific research is increasingly characterised by the volume of documents and data that it produces, from experimental plans and raw data to reports and papers. Researchers frequently struggle to manage and...

    Authors: Samantha Kanza, Nicholas Gibbins and Jeremy G. Frey

    Citation: Journal of Cheminformatics 2019 11:23

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  24. Content type: Research article

    Efficient representations of drugs provide important support for healthcare analytics, such as drug–drug interaction (DDI) prediction and drug–drug similarity (DDS) computation. However, incomplete annotated d...

    Authors: Ying Shen, Kaiqi Yuan, Min Yang, Buzhou Tang, Yaliang Li, Nan Du and Kai Lei

    Citation: Journal of Cheminformatics 2019 11:22

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  25. Content type: Research article

    Recent applications of recurrent neural networks (RNN) enable training models that sample the chemical space. In this study we train RNN with molecular string representations (SMILES) with a subset of the enum...

    Authors: Josep Arús-Pous, Thomas Blaschke, Silas Ulander, Jean-Louis Reymond, Hongming Chen and Ola Engkvist

    Citation: Journal of Cheminformatics 2019 11:20

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  26. Content type: Database

    Drug discovery typically involves investigation of a set of compounds (e.g. drug screening hits) in terms of target, disease, and bioactivity. CSgator is a comprehensive analytic tool for set-wise interpretati...

    Authors: Sera Park, Yeajee Kwon, Hyesoo Jung, Sukyung Jang, Haeseung Lee and Wankyu Kim

    Citation: Journal of Cheminformatics 2019 11:17

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  27. Content type: Review

    Mass spectrometry imaging (MSI) using laser ablation (LA) inductively coupled plasma (ICP) is an innovative and exciting methodology to perform highly sensitive elemental analyses. LA-ICP-MSI of metals, trace ...

    Authors: Ralf Weiskirchen, Sabine Weiskirchen, Philipp Kim and Robert Winkler

    Citation: Journal of Cheminformatics 2019 11:16

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  28. Content type: Research

    Sodium-dependent glucose co-transporter 1 (SGLT1) is a solute carrier responsible for active glucose absorption. SGLT1 is present in both the renal tubules and small intestine. In contrast, the closely related...

    Authors: Lindsey Burggraaff, Paul Oranje, Robin Gouka, Pieter van der Pijl, Marian Geldof, Herman W. T. van Vlijmen, Adriaan P. IJzerman and Gerard J. P. van Westen

    Citation: Journal of Cheminformatics 2019 11:15

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  29. Content type: Software

    Small-molecule protonation can promote or discourage protein binding by altering hydrogen-bond, electrostatic, and van-der-Waals interactions. To improve virtual-screen pose and affinity predictions, researche...

    Authors: Patrick J. Ropp, Jesse C. Kaminsky, Sara Yablonski and Jacob D. Durrant

    Citation: Journal of Cheminformatics 2019 11:14

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  30. Content type: Research article

    Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks of nonribsosomal peptides (NRPs) and as such may give insight into the origin, biosynthesis and bioa...

    Authors: Emma Ricart, Valérie Leclère, Areski Flissi, Markus Mueller, Maude Pupin and Frédérique Lisacek

    Citation: Journal of Cheminformatics 2019 11:13

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  31. Content type: Research article

    OCaml is a functional programming language with strong static types, Hindley–Milner type inference and garbage collection. In this article, we share our experience in prototyping chemoinformatics and structura...

    Authors: Francois Berenger, Kam Y. J. Zhang and Yoshihiro Yamanishi

    Citation: Journal of Cheminformatics 2019 11:10

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  32. Content type: Research article

    In this paper, we explore the impact of combining different in silico prediction approaches and data sources on the predictive performance of the resulting system. We use inhibition of the hERG ion channel tar...

    Authors: Thierry Hanser, Fabian P. Steinmetz, Jeffrey Plante, Friedrich Rippmann and Mireille Krier

    Citation: Journal of Cheminformatics 2019 11:9

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  33. Content type: Research article

    Ligand efficiency is a widely used design parameter in drug discovery. It is calculated by scaling affinity by molecular size and has a nontrivial dependency on the concentration unit used to express affinity ...

    Authors: Peter W. Kenny

    Citation: Journal of Cheminformatics 2019 11:8

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  34. Content type: Research article

    We present a text-mining tool for recognizing biomedical entities in scientific literature. OGER++ is a hybrid system for named entity recognition and concept recognition (linking), which combines a dictionary...

    Authors: Lenz Furrer, Anna Jancso, Nicola Colic and Fabio Rinaldi

    Citation: Journal of Cheminformatics 2019 11:7

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  35. Content type: Preliminary communication

    To facilitate the development of new nanomaterials, especially nanomedicines, a novel computational approach was developed to precisely predict the hydrophobicity of gold nanoparticles (GNPs). The core of this...

    Authors: Wenyi Wang, Xiliang Yan, Linlin Zhao, Daniel P. Russo, Shenqing Wang, Yin Liu, Alexander Sedykh, Xiaoli Zhao, Bing Yan and Hao Zhu

    Citation: Journal of Cheminformatics 2019 11:6

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  36. Content type: Research article

    Biogenic compounds are important materials for drug discovery and chemical biology. In this work, we report a quasi-biogenic molecule generator (QBMG) to compose virtual quasi-biogenic compound libraries by me...

    Authors: Shuangjia Zheng, Xin Yan, Qiong Gu, Yuedong Yang, Yunfei Du, Yutong Lu and Jun Xu

    Citation: Journal of Cheminformatics 2019 11:5

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  37. Content type: Research article

    Structure–activity relationship modelling is frequently used in the early stage of drug discovery to assess the activity of a compound on one or several targets, and can also be used to assess the interaction ...

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

    Citation: Journal of Cheminformatics 2019 11:4

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  38. Content type: Software

    A number of computational tools for metabolism prediction have been developed over the last 20 years to predict the structures of small molecules undergoing biological transformation or environmental degradati...

    Authors: Yannick Djoumbou-Feunang, Jarlei Fiamoncini, Alberto Gil-de-la-Fuente, Russell Greiner, Claudine Manach and David S. Wishart

    Citation: Journal of Cheminformatics 2019 11:2

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  39. Content type: Software

    The need for synthetic route design arises frequently in discovery-oriented chemistry organizations. While traditionally finding solutions to this problem has been the domain of human experts, several computat...

    Authors: Ian A. Watson, Jibo Wang and Christos A. Nicolaou

    Citation: Journal of Cheminformatics 2019 11:1

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  40. Content type: Research article

    The need to efficiently find and extract information from the continuously growing biomedical literature has led to the development of various annotation tools aimed at identifying mentions of entities and rel...

    Authors: Sérgio Matos

    Citation: Journal of Cheminformatics 2018 10:68

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  41. Content type: Meeting report

    The Computational Chemistry List is a mailing list, portal, and community which brings together people interested in computational chemistry, mostly practitioners. It was formed in 1991 and continues to exist ...

    Authors: Frédéric Wieber, Alejandro Pisanty and Alexandre Hocquet

    Citation: Journal of Cheminformatics 2018 10:67

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