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  1. Content type: Software

    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

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  2. Content type: Research article

    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

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  3. Content type: Methodology

    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

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  4. Content type: Research article

    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

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  5. Content type: Software

    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

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  6. Content type: Research article

    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

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  7. Content type: Research article

    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

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  8. Content type: Methodology

    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

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  9. Content type: Software

    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

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. Content type: Research article

    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

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  13. Content type: Preliminary communication

    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

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  14. Content type: Research article

    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

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  15. Content type: Database

    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

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  16. Content type: Software

    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

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  17. Content type: Software

    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

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  18. Content type: Preliminary communication

    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

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  19. Content type: Research article

    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

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  20. Content type: Software

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Software

    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

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  26. Content type: Database

    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

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  27. Content type: Database

    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

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  28. Content type: Software

    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

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  29. Content type: Research article

    It is now widely recognized that there is an urgent need for new antibacterial drugs, with novel mechanisms of action, to combat the rise of multi-drug resistant bacteria. However, few new compounds are reachi...

    Authors: Jean-Paul Ebejer, Michael H. Charlton and Paul W. Finn

    Citation: Journal of Cheminformatics 2016 8:30

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  30. Content type: Research article

    Bioassay data analysis continues to be an essential, routine, yet challenging task in modern drug discovery and chemical biology research. The challenge is to infer reliable knowledge from big and noisy data. ...

    Authors: Jeremy J. Yang, Oleg Ursu, Christopher A. Lipinski, Larry A. Sklar, Tudor I. Oprea and Cristian G. Bologa

    Citation: Journal of Cheminformatics 2016 8:29

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  31. Content type: Software

    Halogen bonding has recently come to play as a target for lead optimization in rational drug design. However, most docking program don’t account for halogen bonding in their scoring functions and are not able ...

    Authors: Mathew R. Koebel, Grant Schmadeke, Richard G. Posner and Suman Sirimulla

    Citation: Journal of Cheminformatics 2016 8:27

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  32. Content type: Research article

    We present “Ask Ernö”, a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component i...

    Authors: Andrés M. Castillo, Andrés Bernal, Reiner Dieden, Luc Patiny and Julien Wist

    Citation: Journal of Cheminformatics 2016 8:26

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  33. Content type: Database

    Similarly to the periodic table for elements, chemical space offers an organizing principle for representing the diversity of organic molecules, usually in the form of multi-dimensional property spaces that ar...

    Authors: Mahendra Awale and Jean-Louis Reymond

    Citation: Journal of Cheminformatics 2016 8:25

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  34. Content type: Research article

    Non-covalent interactions (NCIs) play critical roles in supramolecular chemistries; however, they are difficult to measure. Currently, reliable computational methods are being pursued to meet this challenge, ...

    Authors: Ting Gao, Hongzhi Li, Wenze Li, Lin Li, Chao Fang, Hui Li, LiHong Hu, Yinghua Lu and Zhong-Min Su

    Citation: Journal of Cheminformatics 2016 8:24

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  35. Content type: Methodology

    This study seeks to develop, test and assess a methodology for automatic extraction of a complete set of ‘term-like phrases’ and to create a terminology spectrum from a collection of natural language PDF docum...

    Authors: Boris L. Alperin, Andrey O. Kuzmin, Ludmila Yu. Ilina, Vladimir D. Gusev, Natalia V. Salomatina and Valentin N. Parmon

    Citation: Journal of Cheminformatics 2016 8:22

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  36. Content type: Meeting abstracts

    Authors: Uli Fechner, Chris de Graaf, Andrew E. Torda, Stefan Güssregen, Andreas Evers, Hans Matter, Gerhard Hessler, Nicola J. Richmond, Peter Schmidtke, Marwin H. S. Segler, Mark P. Waller, Stefanie Pleik, Joan-Emma Shea, Zachary Levine, Ryan Mullen, Karina van den Broek…

    Citation: Journal of Cheminformatics 2016 8(Suppl 1):18

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    This article is part of a Supplement: Volume 8 Supplement 1

  37. Content type: Research article

    In silico target prediction of compounds plays an important role in drug discovery. The chemical similarity ensemble approach (SEA) is a promising method, which has been successfully applied in many drug-relat...

    Authors: Zhonghua Wang, Lu Liang, Zheng Yin and Jianping Lin

    Citation: Journal of Cheminformatics 2016 8:20

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  38. Content type: Software

    Since the structure of proteins is more conserved than the sequence, the identification of conserved three-dimensional (3D) patterns among a set of proteins, can be important for protein function prediction, p...

    Authors: Gabriel Núñez-Vivanco, Alejandro Valdés-Jiménez, Felipe Besoaín and Miguel Reyes-Parada

    Citation: Journal of Cheminformatics 2016 8:19

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  39. Content type: Software

    Disordered compounds are crucially important for fundamental science and industrial applications. Yet most available methods to explore solid-state material properties require ideal periodicity, which, strictl...

    Authors: Kirill Okhotnikov, Thibault Charpentier and Sylvian Cadars

    Citation: Journal of Cheminformatics 2016 8:17

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  40. Content type: Research article

    Complex network theory based methods and the emergence of “Big Data” have reshaped the terrain of investigating structure-activity relationships of molecules. This change gave rise to new methods which need to...

    Authors: Gergely Zahoránszky-Kőhalmi, Cristian G. Bologa and Tudor I. Oprea

    Citation: Journal of Cheminformatics 2016 8:16

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    The Erratum to this article has been published in Journal of Cheminformatics 2016 8:28

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