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  1. Content type: Research article

    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

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  2. Content type: Research article

    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

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  3. Content type: Software

    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

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  4. Content type: Software

    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

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  5. Content type: Research article

    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

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  6. Content type: Research article

    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

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  7. Content type: Research article

    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

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  8. Content type: Research article

    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

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  9. Content type: Research article

    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

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  10. Content type: Research

    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

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  11. Content type: Database

    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

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  12. Content type: Research article

    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

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  13. Content type: Software

    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

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  14. Content type: Research article

    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

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  15. Content type: Research article

    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

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  16. Content type: Research article

    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

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  17. Content type: Research article

    The collection of chemical structure information and associated experimental data for quantitative structure–activity/property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public...

    Authors: Kamel Mansouri, Chris M. Grulke, Richard S. Judson and Antony J. Williams

    Citation: Journal of Cheminformatics 2018 10:10

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  18. Content type: Research article

    Spectrophores are novel descriptors that are calculated from the three-dimensional atomic properties of molecules. In our current implementation, the atomic properties that were used to calculate spectrophores...

    Authors: Rafaela Gladysz, Fabio Mendes Dos Santos, Wilfried Langenaeker, Gert Thijs, Koen Augustyns and Hans De Winter

    Citation: Journal of Cheminformatics 2018 10:9

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  19. Content type: Methodology

    Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out ...

    Authors: Laeeq Ahmed, Valentin Georgiev, Marco Capuccini, Salman Toor, Wesley Schaal, Erwin Laure and Ola Spjuth

    Citation: Journal of Cheminformatics 2018 10:8

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  20. Content type: Research article

    Iterative screening has emerged as a promising approach to increase the efficiency of screening campaigns compared to traditional high throughput approaches. By learning from a subset of the compound library, ...

    Authors: Fredrik Svensson, Avid M. Afzal, Ulf Norinder and Andreas Bender

    Citation: Journal of Cheminformatics 2018 10:7

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  21. Content type: Research article

    Given that many antifungal medications are susceptible to evolved resistance, there is a need for novel drugs with unique mechanisms of action. Inhibiting the essential proton pump Pma1p, a P-type ATPase, is a...

    Authors: Sabine Ottilie, Gregory M. Goldgof, Andrea L. Cheung, Jennifer L. Walker, Edgar Vigil, Kenneth E. Allen, Yevgeniya Antonova-Koch, Carolyn W. Slayman, Yo Suzuki and Jacob D. Durrant

    Citation: Journal of Cheminformatics 2018 10:6

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  22. Content type: Review

    OriginLab’s newest version update to Origin and OriginPro includes ease-of-use features, like Origin Central updates and creation of an App Center, as well as larger changes like the addition of Unicode charac...

    Authors: James G. Moberly, Matthew T. Bernards and Kristopher V. Waynant

    Citation: Journal of Cheminformatics 2018 10:5

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  23. Content type: Software

    Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Various molecular-descriptor-calculation software programs have been developed. However, users of those progra...

    Authors: Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita and Tatsuya Takagi

    Citation: Journal of Cheminformatics 2018 10:4

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  24. Content type: Research article

    Idiosyncratic adverse drug reactions have been linked to a drug’s ability to bind with a human leukocyte antigen (HLA) protein. However, due to the thousands of HLA variants and limited structural data for dru...

    Authors: George Van Den Driessche and Denis Fourches

    Citation: Journal of Cheminformatics 2018 10:3

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  25. Content type: Research article

    Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, inclu...

    Authors: Sehan Lee and Mace G. Barron

    Citation: Journal of Cheminformatics 2018 10:2

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  26. Content type: Research article

    In-silico quantitative structure–activity relationship (QSAR) models based tools are widely used to screen huge databases of compounds in order to determine the biological properties of chemical molecules base...

    Authors: Samina Kausar and Andre O. Falcao

    Citation: Journal of Cheminformatics 2018 10:1

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  27. Content type: Research article

    Compounds designed to display polypharmacology may have utility in treating complex diseases, where activity at multiple targets is required to produce a clinical effect. In particular, suitable compounds may ...

    Authors: Leen Kalash, Cristina Val, Jhonny Azuaje, María I. Loza, Fredrik Svensson, Azedine Zoufir, Lewis Mervin, Graham Ladds, José Brea, Robert Glen, Eddy Sotelo and Andreas Bender

    Citation: Journal of Cheminformatics 2017 9:67

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  28. Content type: Research article

    Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for...

    Authors: Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu and Tingjun Hou

    Citation: Journal of Cheminformatics 2017 9:66

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  29. Content type: Methodology

    Targets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple bin...

    Authors: Mónika Bálint, Norbert Jeszenői, István Horváth, David van der Spoel and Csaba Hetényi

    Citation: Journal of Cheminformatics 2017 9:65

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  30. Content type: Methodology

    Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a s...

    Authors: Mathilde Koch, Thomas Duigou, Pablo Carbonell and Jean-Loup Faulon

    Citation: Journal of Cheminformatics 2017 9:64

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  31. Content type: Research article

    In this study, we design and carry out a survey, asking human experts to predict the aqueous solubility of druglike organic compounds. We investigate whether these experts, drawn largely from the pharmaceutica...

    Authors: Samuel Boobier, Anne Osbourn and John B. O. Mitchell

    Citation: Journal of Cheminformatics 2017 9:63

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  32. Content type: Software

    We describe a novel freely available web server Base of Bioisosterically Exchangeable Replacements (BoBER), which implements an interface to a database of bioisosteric and scaffold hopping replacements. Bioiso...

    Authors: Samo Lešnik, Blaž Škrlj, Nika Eržen, Urban Bren, Stanislav Gobec, Janez Konc and Dušanka Janežič

    Citation: Journal of Cheminformatics 2017 9:62

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  33. Content type: Database

    Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and co...

    Authors: Antony J. Williams, Christopher M. Grulke, Jeff Edwards, Andrew D. McEachran, Kamel Mansouri, Nancy C. Baker, Grace Patlewicz, Imran Shah, John F. Wambaugh, Richard S. Judson and Ann M. Richard

    Citation: Journal of Cheminformatics 2017 9:61

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  34. Content type: Research Article

    In ligand-based virtual screening experiments, a known active ligand is used in similarity searches to find putative active compounds for the same protein target. When there are several known active molecules,...

    Authors: Francois Berenger, Oanh Vu and Jens Meiler

    Citation: Journal of Cheminformatics 2017 9:60

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  35. Content type: Software

    Computational methods to predict binding affinities of small ligands toward relevant biological (off-)targets are helpful in prioritizing the screening and synthesis of new drug candidates, thereby speeding up...

    Authors: Luigi Capoferri, Marc van Dijk, Ariën S. Rustenburg, Tsjerk A. Wassenaar, Derk P. Kooi, Eko A. Rifai, Nico P. E. Vermeulen and Daan P. Geerke

    Citation: Journal of Cheminformatics 2017 9:58

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  36. Content type: Research article

    The identification of chemical structures in natural product mixtures is an important task in drug discovery but is still a challenging problem, as structural elucidation is a time-consuming process and is li...

    Authors: Bo-Han Su, Meng-Yu Shen, Yeu-Chern Harn, San-Yuan Wang, Alioune Schurz, Chieh Lin, Olivia A. Lin and Yufeng J. Tseng

    Citation: Journal of Cheminformatics 2017 9:57

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  37. Content type: Research article

    In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of tech...

    Authors: Andrius Merkys, Nicolas Mounet, Andrea Cepellotti, Nicola Marzari, Saulius Gražulis and Giovanni Pizzi

    Citation: Journal of Cheminformatics 2017 9:56

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  38. Content type: Software

    The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern ...

    Authors: Pierre Tremouilhac, An Nguyen, Yu-Chieh Huang, Serhii Kotov, Dominic Sebastian Lütjohann, Florian Hübsch, Nicole Jung and Stefan Bräse

    Citation: Journal of Cheminformatics 2017 9:54

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  39. Content type: Erratum

    Authors: Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomáš Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain Torrance, Chris T. Evelo, Rajarshi Guha and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2017 9:53

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    The original article was published in Journal of Cheminformatics 2017 9:33

  40. Content type: Software

    Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with depende...

    Authors: Patrick Ropp, Aaron Friedman and Jacob D. Durrant

    Citation: Journal of Cheminformatics 2017 9:52

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  41. Content type: Review

    Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synth...

    Authors: Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett and Lydia E. Kavraki

    Citation: Journal of Cheminformatics 2017 9:51

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  42. Content type: Research Article

    GPU acceleration is useful in solving complex chemical information problems. Identifying unknown structures from the mass spectra of natural product mixtures has been a desirable yet unresolved issue in metabo...

    Authors: Alioune Schurz, Bo-Han Su, Yi-Shu Tu, Tony Tsung-Yu Lu, Olivia A. Lin and Yufeng J. Tseng

    Citation: Journal of Cheminformatics 2017 9:50

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  43. Content type: Preliminary communication

    On the one hand, ligand efficiency (LE) and the binding efficiency index (BEI), which are binding properties (B) averaged versus the heavy atom count (HAC: LE) or molecular weight (MW: BEI), have recently been...

    Authors: Jaroslaw Polanski, Aleksandra Tkocz and Urszula Kucia

    Citation: Journal of Cheminformatics 2017 9:49

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