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  1. 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 Published on:

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

  2. 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 Published on:

  3. 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 Published on:

  4. 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 Published on:

  5. 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 Published on:

  6. 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 Published on:

  9. 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 Published on:

  11. 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 Published on:

  12. 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 Published on:

  13. 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 Published on:

  14. 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 Published on:

  15. 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 Published on:

  16. 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 Published on:

  17. 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 Published on:

  18. 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 Published on:

  19. 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 Published on:

  20. 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 Published on:

  21. 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 Published on:

  22. 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 Published on:

  23. 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 Published on:

  24. 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 Published on:

  25. 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 Published on:

  29. 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 Published on:

  30. 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 Published on:

  32. 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 Published on:

  33. 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 Published on:

  34. 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:

  35. 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:

  36. 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:

  37. 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 Published on:

  38. 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 Published on:

  39. 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 Published on:

  41. 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 Published on:

  42. 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 Published on:

  43. 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 Published on:

  46. Drug-target identification is crucial to discover novel applications for existing drugs and provide more insights about mechanisms of biological actions, such as adverse drug effects (ADEs). Computational meth...

    Authors: Santiago Vilar and George Hripcsak
    Citation: Journal of Cheminformatics 2016 8:35
    Content type: Research article Published on:

  47. More and more evidences from network biology indicate that most cellular components exert their functions through interactions with other cellular components, such as proteins, DNAs, RNAs and small molecules. ...

    Authors: Jie Dong, Zhi-Jiang Yao, Ming Wen, Min-Feng Zhu, Ning-Ning Wang, Hong-Yu Miao, Ai-Ping Lu, Wen-Bin Zeng and Dong-Sheng Cao
    Citation: Journal of Cheminformatics 2016 8:34
    Content type: Software Published on:

  48. The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failur...

    Authors: Ashenafi Legehar, Henri Xhaard and Leo Ghemtio
    Citation: Journal of Cheminformatics 2016 8:33
    Content type: Database Published on:

  49. PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, l...

    Authors: Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Bo Yu, Benjamin A. Shoemaker, Jiyao Wang, Evan E. Bolton, Yanli Wang and Stephen H. Bryant
    Citation: Journal of Cheminformatics 2016 8:32
    Content type: Database Published on:

  50. In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better...

    Authors: Jakub Galgonek, Tomáš Hurt, Vendula Michlíková, Petr Onderka, Jan Schwarz and Jiří Vondrášek
    Citation: Journal of Cheminformatics 2016 8:31
    Content type: Software Published on:
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