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  1. Several web-based tools have been reported recently which predict the possible targets of a small molecule by similarity to compounds of known bioactivity using molecular fingerprints (fps), however predictio...

    Authors: Mahendra Awale and Jean-Louis Reymond

    Citation: Journal of Cheminformatics 2017 9:11

    Content type: Methodology

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  2. The symbols for the new IUPAC elements named in November 2016 can introduce subtle ambiguities within cheminformatics software. The ambiguities are described and demonstrated by highlighting inconsistencies be...

    Authors: John W. Mayfield and Roger A. Sayle

    Citation: Journal of Cheminformatics 2017 9:10

    Content type: Commentary

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  3. Molecular fingerprints are widely used in several areas of chemoinformatics including diversity analysis and similarity searching. The fingerprint-based analysis of chemical libraries, in particular of large c...

    Authors: Eli Fernández-de Gortari, César R. García-Jacas, Karina Martinez-Mayorga and José L. Medina-Franco

    Citation: Journal of Cheminformatics 2017 9:9

    Content type: Preliminary communication

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  4. A new metric for the evaluation of model performance in the field of virtual screening and quantitative structure–activity relationship applications is described. This metric has been termed the power metric a...

    Authors: Julio Cesar Dias Lopes, Fábio Mendes dos Santos, Andrelly Martins-José, Koen Augustyns and Hans De Winter

    Citation: Journal of Cheminformatics 2017 9:7

    Content type: Research article

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    The Commentary to this article has been published in Journal of Cheminformatics 2018 10:13

  5. High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and p...

    Authors: Sandip De, Felix Musil, Teresa Ingram, Carsten Baldauf and Michele Ceriotti

    Citation: Journal of Cheminformatics 2017 9:6

    Content type: Research article

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  6. Skin sensitization is an important toxicological endpoint for chemical hazard determination and safety assessment. Prediction of chemical skin sensitizer had traditionally relied on data from rodent models. Th...

    Authors: Chia-Chi Wang, Ying-Chi Lin, Shan-Shan Wang, Chieh Shih, Yi-Hui Lin and Chun-Wei Tung

    Citation: Journal of Cheminformatics 2017 9:5

    Content type: Database

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  7. The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with Dat...

    Authors: Matthew J. Harvey, Andrew McLean and Henry S. Rzepa

    Citation: Journal of Cheminformatics 2017 9:4

    Content type: Research article

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  8. Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ1) and sigma-2 (σ2). The two receptor subtypes have specific drug actions, pharmacological profiles and molec...

    Authors: Giovanni Nastasi, Carla Miceli, Valeria Pittalà, Maria N. Modica, Orazio Prezzavento, Giuseppe Romeo, Antonio Rescifina, Agostino Marrazzo and Emanuele Amata

    Citation: Journal of Cheminformatics 2017 9:3

    Content type: Database

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  9. Natural products have increasingly attracted much attention as a valuable resource for the development of anticancer medicines due to the structural novelty and good bioavailability. This necessitates a compr...

    Authors: Hwanho Choi, Sun Young Cho, Ho Jeong Pak, Youngsoo Kim, Jung-yun Choi, Yoon Jae Lee, Byung Hee Gong, Yeon Seok Kang, Taehoon Han, Geunbae Choi, Yeeun Cho, Soomin Lee, Dekwoo Ryoo and Hwangseo Park

    Citation: Journal of Cheminformatics 2017 9:2

    Content type: Database

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  10. Molecular descriptors have been widely used to predict biological activities and physicochemical properties or to analyze chemical libraries on the basis of similarity. Although fingerprints and properties are...

    Authors: Masataka Kuroda

    Citation: Journal of Cheminformatics 2017 9:1

    Content type: Research article

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  11. Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligom...

    Authors: Saw Simeon, Watshara Shoombuatong, Nuttapat Anuwongcharoen, Likit Preeyanon, Virapong Prachayasittikul, Jarl E. S. Wikberg and Chanin Nantasenamat

    Citation: Journal of Cheminformatics 2016 8:72

    Content type: Research article

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  12. Analysis of the 3D structures of protein–ligand binding sites can provide valuable insights for drug discovery. Binding site comparison (BSC) studies can be employed to elucidate the function of orphan protein...

    Authors: Joshua Meyers, Nathan Brown and Julian Blagg

    Citation: Journal of Cheminformatics 2016 8:70

    Content type: Research article

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  13. The ability to define the regions of chemical space where a predictive model can be safely used is a necessary condition to assure the reliability of new predictions. This implies that reliability must be dete...

    Authors: Natália Aniceto, Alex A. Freitas, Andreas Bender and Taravat Ghafourian

    Citation: Journal of Cheminformatics 2016 8:69

    Content type: Methodology

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  14. The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site o...

    Authors: Anastasia V. Rudik, Alexander V. Dmitriev, Alexey A. Lagunin, Dmitry A. Filimonov and Vladimir V. Poroikov

    Citation: Journal of Cheminformatics 2016 8:68

    Content type: Research Article

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  15. Predictive modelling in drug discovery is challenging to automate as it often contains multiple analysis steps and might involve cross-validation and parameter tuning that create complex dependencies between ...

    Authors: Samuel Lampa, Jonathan Alvarsson and Ola Spjuth

    Citation: Journal of Cheminformatics 2016 8:67

    Content type: Methodology

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  16. Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious....

    Authors: Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie and Jason E. Bara

    Citation: Journal of Cheminformatics 2016 8:66

    Content type: Methodology

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  17. The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution im...

    Authors: Hugo López-Fernández, Gustavo de S. Pessôa, Marco A. Z. Arruda, José L. Capelo-Martínez, Florentino Fdez-Riverola, Daniel Glez-Peña and Miguel Reboiro-Jato

    Citation: Journal of Cheminformatics 2016 8:65

    Content type: Software

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  18. Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitabl...

    Authors: Othman Soufan, Wail Ba-Alawi, Moataz Afeef, Magbubah Essack, Panos Kalnis and Vladimir B. Bajic

    Citation: Journal of Cheminformatics 2016 8:64

    Content type: Research article

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  19. Measuring the structural diversity of compound databases is relevant in drug discovery and many other areas of chemistry. Since molecular diversity depends on molecular representation, comprehensive chemoinfor...

    Authors: Mariana González-Medina, Fernando D. Prieto-Martínez, John R. Owen and José L. Medina-Franco

    Citation: Journal of Cheminformatics 2016 8:63

    Content type: Methodology

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  20. PubChem is a public repository for biological activities of small molecules. For the efficient use of its vast amount of chemical information, PubChem performs 2-dimensional (2-D) and 3-dimensional (3-D) neigh...

    Authors: Sunghwan Kim, Evan E. Bolton and Stephen H. Bryant

    Citation: Journal of Cheminformatics 2016 8:62

    Content type: Research article

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  21. Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, t...

    Authors: Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner and David S. Wishart

    Citation: Journal of Cheminformatics 2016 8:61

    Content type: Software

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  22. Even though circular fingerprints have been first introduced more than 50 years ago, they are still widely used for building highly predictive, state-of-the-art (Q)SAR models. Historically, these structural fr...

    Authors: Martin Gütlein and Stefan Kramer

    Citation: Journal of Cheminformatics 2016 8:60

    Content type: Research article

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  23. Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER f...

    Authors: Maryam Habibi, David Luis Wiegandt, Florian Schmedding and Ulf Leser

    Citation: Journal of Cheminformatics 2016 8:59

    Content type: Research article

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  24. In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. T...

    Authors: Junaid Arshad, Alexander Hoffmann, Sandra Gesing, Richard Grunzke, Jens Krüger, Tamas Kiss, Sonja Herres-Pawlis and Gabor Terstyanszky

    Citation: Journal of Cheminformatics 2016 8:58

    Content type: Methodology

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  25. The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equal...

    Authors: Tomáš Raček, Jana Pazúriková, Radka Svobodová Vařeková, Stanislav Geidl, Aleš Křenek, Francesco Luca Falginella, Vladimír Horský, Václav Hejret and Jaroslav Koča

    Citation: Journal of Cheminformatics 2016 8:57

    Content type: Software

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  26. In a structure-based virtual screening, the choice of the docking program is essential for the success of a hit identification. Benchmarks are meant to help in guiding this choice, especially when undertaken ...

    Authors: Ludovic Chaput, Juan Martinez-Sanz, Nicolas Saettel and Liliane Mouawad

    Citation: Journal of Cheminformatics 2016 8:56

    Content type: Research article

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  27. This bibliometric study aims to analyze the publications in which density functional theory (DFT) plays a major role. The bibliometric analysis is performed on the full publication volume of 114,138 publicatio...

    Authors: Robin Haunschild, Andreas Barth and Werner Marx

    Citation: Journal of Cheminformatics 2016 8:52

    Content type: Research article

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  28. With a constant increase in the number of new chemicals synthesized every year, it becomes important to employ the most reliable and fast in silico screening methods to predict their safety and activity profil...

    Authors: Priyanka Banerjee, Vishal B. Siramshetty, Malgorzata N. Drwal and Robert Preissner

    Citation: Journal of Cheminformatics 2016 8:51

    Content type: Research article

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  29. This communication deals with the scientific problem of evaluating the similarity between two chemical systems, each described by a finite discrete set of elements/members, which are in turn p-dimensional vectors...

    Authors: Andrea Mauri, Davide Ballabio, Roberto Todeschini and Viviana Consonni

    Citation: Journal of Cheminformatics 2016 8:49

    Content type: Preliminary communication

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  30. Quantitative structure activity relationships (QSARs) are theoretical models that relate a quantitative measure of chemical structure to a physical property or a biological effect. QSAR predictions can be used...

    Authors: Prachi Pradeep, Richard J. Povinelli, Shannon White and Stephen J. Merrill

    Citation: Journal of Cheminformatics 2016 8:48

    Content type: Research article

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  31. Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly avail...

    Authors: Ola Spjuth, Patrik Rydberg, Egon L. Willighagen, Chris T. Evelo and Nina Jeliazkova

    Citation: Journal of Cheminformatics 2016 8:47

    Content type: Database

    Published on:

  32. Ligand-based virtual screening of large small-molecule databases is an important step in the early stages of drug development. It is based on the similarity principle and is used to reduce the chemical space o...

    Authors: Athira Dilip, Samo Lešnik, Tanja Štular, Dušanka Janežič and Janez Konc

    Citation: Journal of Cheminformatics 2016 8:46

    Content type: Software

    Published on:

  33. Receiver operating characteristics (ROC) curve with the calculation of area under curve (AUC) is a useful tool to evaluate the performance of biomedical and chemoinformatics data. For example, in virtual drug...

    Authors: Sakari Lätti, Sanna Niinivehmas and Olli T. Pentikäinen

    Citation: Journal of Cheminformatics 2016 8:45

    Content type: Software

    Published on:

  34. Liquid chromatography-high resolution mass spectrometry (LC-MS) has emerged as one of the most widely used platforms for untargeted metabolomics due to its unparalleled sensitivity and metabolite coverage. Des...

    Authors: A. McMillan, J. B. Renaud, G. B. Gloor, G. Reid and M. W. Sumarah

    Citation: Journal of Cheminformatics 2016 8:44

    Content type: Preliminary communication

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  35. Nuclear receptors (NRs) constitute an important class of therapeutic targets. We evaluated the performance of 3D structure-based and ligand-based pharmacophore models in predicting the pharmacological profile ...

    Authors: Nathalie Lagarde, Solenne Delahaye, Jean-François Zagury and Matthieu Montes

    Citation: Journal of Cheminformatics 2016 8:43

    Content type: Research article

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  36. We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan an...

    Authors: Gert-Jan Bekker, Haruki Nakamura and Akira R. Kinjo

    Citation: Journal of Cheminformatics 2016 8:42

    Content type: Software

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  37. Ionic liquids (ILs) found a variety of applications in today’s chemistry. Since their properties depend on the ions constituting particular ionic liquid, it is possible to synthetize IL with desired specificat...

    Authors: Maciej Barycki, Anita Sosnowska, Magdalena Piotrowska, Piotr Urbaszek, Anna Rybinska, Monika Grzonkowska and Tomasz Puzyn

    Citation: Journal of Cheminformatics 2016 8:40

    Content type: Research article

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  38. The increasing size of datasets in drug discovery makes it challenging to build robust and accurate predictive models within a reasonable amount of time. In order to investigate the effect of dataset sizes on ...

    Authors: Jonathan Alvarsson, Samuel Lampa, Wesley Schaal, Claes Andersson, Jarl E. S. Wikberg and Ola Spjuth

    Citation: Journal of Cheminformatics 2016 8:39

    Content type: Research article

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  39. Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algo...

    Authors: Jun Gao, Qingchen Zhang, Min Liu, Lixin Zhu, Dingfeng Wu, Zhiwei Cao and Ruixin Zhu

    Citation: Journal of Cheminformatics 2016 8:38

    Content type: Research article

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