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  1. 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

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  2. 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

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  3. 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

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  4. 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

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  5. 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

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  6. 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

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  7. 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

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  8. 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

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  9. 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

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

  10. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. 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

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  17. 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

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  18. 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

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  19. 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

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  20. 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

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  21. 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

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  22. 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:

  23. 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

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  24. 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

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  25. 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

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  26. 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

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  27. 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

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  28. 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

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  29. 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

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  30. 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

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  31. 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

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  32. 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:

  33. 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

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  34. 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

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  35. 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

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  36. 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

    Content type: Research article

    Published on:

  37. 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

    Content type: Research article

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  38. 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

    Content type: Methodology

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  39. 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

    Content type: Research article

    Published on:

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