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  1. 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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  2. 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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  3. 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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  4. 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

  5. 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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  6. 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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  7. 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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  8. 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

  9. Content type: Research article

    Identification of novel drug–target interactions (DTIs) is important for drug discovery. Experimental determination of such DTIs is costly and time consuming, hence it necessitates the development of efficient...

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

    Citation: Journal of Cheminformatics 2016 8:15

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  10. Content type: Software

    Due to exorbitant costs of high-throughput screening, many drug discovery projects commonly employ inexpensive virtual screening to support experimental efforts. However, the vast majority of compounds in wide...

    Authors: Misagh Naderi, Chris Alvin, Yun Ding, Supratik Mukhopadhyay and Michal Brylinski

    Citation: Journal of Cheminformatics 2016 8:14

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  11. Content type: Software

    ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, dat...

    Authors: Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John May, Christoph Steinbeck and Pedro Mendes

    Citation: Journal of Cheminformatics 2016 8:11

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  12. Content type: Research article

    Recently, novel 3D alignment-free molecular descriptors (also known as QuBiLS-MIDAS) based on two-linear, three-linear and four-linear algebraic forms have been introduced. These descriptors codify chemical in...

    Authors: César R. García-Jacas, Ernesto Contreras-Torres, Yovani Marrero-Ponce, Mario Pupo-Meriño, Stephen J. Barigye and Lisset Cabrera-Leyva

    Citation: Journal of Cheminformatics 2016 8:10

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  13. Content type: Methodology

    The testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory...

    Authors: David M. L. Brown, Herman Cho and Wibe A. de Jong

    Citation: Journal of Cheminformatics 2016 8:8

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  14. Content type: Research article

    The human ATP binding cassette transporters Breast Cancer Resistance Protein (BCRP) and Multidrug Resistance Protein 1 (P-gp) are co-expressed in many tissues and barriers, especially at the blood–brain barrie...

    Authors: Floriane Montanari, Barbara Zdrazil, Daniela Digles and Gerhard F. Ecker

    Citation: Journal of Cheminformatics 2016 8:7

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  15. Content type: Research article

    Determination of acute toxicity, expressed as median lethal dose (LD50), is one of the most important steps in drug discovery pipeline. Because in vivo assays for oral acute toxicity in mammals are time-consumin...

    Authors: Tailong Lei, Youyong Li, Yunlong Song, Dan Li, Huiyong Sun and Tingjun Hou

    Citation: Journal of Cheminformatics 2016 8:6

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  16. Content type: Research Article

    Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds....

    Authors: Sebastian Böcker and Kai Dührkop

    Citation: Journal of Cheminformatics 2016 8:5

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  17. Content type: Software

    The in silico fragmenter MetFrag, launched in 2010, was one of the first approaches combining compound database searching and fragmentation prediction for small molecule identification from tandem mass spectromet...

    Authors: Christoph Ruttkies, Emma L. Schymanski, Sebastian Wolf, Juliane Hollender and Steffen Neumann

    Citation: Journal of Cheminformatics 2016 8:3

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  18. Content type: Research article

    Hierarchical cluster analysis (HCA) is a widely used classificatory technique in many areas of scientific knowledge. Applications usually yield a dendrogram from an HCA run over a given data set, using a group...

    Authors: Wilmer Leal, Eugenio J. Llanos, Guillermo Restrepo, Carlos F. Suárez and Manuel Elkin Patarroyo

    Citation: Journal of Cheminformatics 2016 8:4

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  19. Content type: Research Article

    Melting point (MP) is an important property in regards to the solubility of chemical compounds. Its prediction from chemical structure remains a highly challenging task for quantitative structure–activity rel...

    Authors: Igor V. Tetko, Daniel M. Lowe and Antony J. Williams

    Citation: Journal of Cheminformatics 2016 8:2

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  20. Content type: Research article

    In drug design, one may be confronted to the problem of finding hits for targets for which no small inhibiting molecules are known and only low-throughput experiments are available (like ITC or NMR studies), t...

    Authors: Ludovic Chaput, Juan Martinez-Sanz, Eric Quiniou, Pascal Rigolet, Nicolas Saettel and Liliane Mouawad

    Citation: Journal of Cheminformatics 2016 8:1

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  21. Content type: Research article

    A number of algorithms have been proposed to predict the biological targets of diverse molecules. Some are structure-based, but the most common are ligand-based and use chemical fingerprints and the notion of...

    Authors: Alessandro Lusci, David Fooshee, Michael Browning, Joshua Swamidass and Pierre Baldi

    Citation: Journal of Cheminformatics 2015 7:63

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  22. Content type: Software

    Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calc...

    Authors: Jie Dong, Dong-Sheng Cao, Hong-Yu Miao, Shao Liu, Bai-Chuan Deng, Yong-Huan Yun, Ning-Ning Wang, Ai-Ping Lu, Wen-Bin Zeng and Alex F. Chen

    Citation: Journal of Cheminformatics 2015 7:60

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  23. Content type: Research article

    Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinform...

    Authors: Stanislav Geidl, Tomáš Bouchal, Tomáš Raček, Radka Svobodová Vařeková, Václav Hejret, Aleš Křenek, Ruben Abagyan and Jaroslav Koča

    Citation: Journal of Cheminformatics 2015 7:59

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  24. Content type: Commentary

    It is common in cheminformatics to represent the properties of a ligand as a string of 1’s and 0’s, with the intention of elucidating, inter alia, the relationship between the chemical structure of a ligand and i...

    Authors: Hamse Y. Mussa, John B. O. Mitchell and Robert C. Glen

    Citation: Journal of Cheminformatics 2015 7:58

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  25. Content type: Research article

    The formation of intramolecular hydrogen bonds (IHBs) may induce the remarkable changes in molecular physicochemical properties. Within the framework of the extended solvent-contact model, we investigate the e...

    Authors: Kee-Choo Chung and Hwangseo Park

    Citation: Journal of Cheminformatics 2015 7:57

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  26. Content type: Research article

    The enriched biological activity information of compounds in large and freely-accessible chemical databases like the PubChem Bioassay Database has become a powerful research resource for the scientific researc...

    Authors: Xiang Yu, Lewis Y. Geer, Lianyi Han and Stephen H. Bryant

    Citation: Journal of Cheminformatics 2015 7:55

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  27. Content type: Research article

    A wide range of chemical compound databases are currently available for pharmaceutical research. To retrieve compound information, including structures, researchers can query these chemical databases using non...

    Authors: Saber A. Akhondi, Sorel Muresan, Antony J. Williams and Jan A. Kors

    Citation: Journal of Cheminformatics 2015 7:54

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  28. Content type: Research article

    A new lipid class named ‘fatty acid esters of hydroxyl fatty acids’ (FAHFA) was recently discovered in mammalian adipose tissue and in blood plasma and some FAHFAs were found to be associated with type 2 diabe...

    Authors: Yan Ma, Tobias Kind, Arpana Vaniya, Ingrid Gennity, Johannes F. Fahrmann and Oliver Fiehn

    Citation: Journal of Cheminformatics 2015 7:53

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  29. Content type: Research article

    In the present work, we aim to transfer to the field of virtual screening the predictiveness curve, a metric that has been advocated in clinical epidemiology. The literature describes the use of predictiveness...

    Authors: Charly Empereur-mot, Hélène Guillemain, Aurélien Latouche, Jean-François Zagury, Vivian Viallon and Matthieu Montes

    Citation: Journal of Cheminformatics 2015 7:52

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  30. Content type: Research article

    In silico analyses are increasingly being used to support mode-of-action investigations; however many such approaches do not utilise the large amounts of inactive data held in chemogenomic repositories. The ob...

    Authors: Lewis H. Mervin, Avid M. Afzal, Georgios Drakakis, Richard Lewis, Ola Engkvist and Andreas Bender

    Citation: Journal of Cheminformatics 2015 7:51

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  31. Content type: Software

    Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.

    Authors: Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukáš Pravda, Tomáš Bouchal, Radka Svobodová Vařeková, Stanislav Geidl and Jaroslav Koča

    Citation: Journal of Cheminformatics 2015 7:50

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  32. Content type: Research article

    First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual proces...

    Authors: Stefan Senger, Luca Bartek, George Papadatos and Anna Gaulton

    Citation: Journal of Cheminformatics 2015 7:49

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  33. Content type: Review

    Enzymes are one of the most important groups of drug targets, and identifying possible ligand-enzyme interactions is of major importance in many drug discovery processes. Novel computational methods have been ...

    Authors: Janez Konc, Samo Lešnik and Dušanka Janežič

    Citation: Journal of Cheminformatics 2015 7:48

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  34. Content type: Software

    The interaction of a small molecule with a protein target depends on its ability to adopt a three-dimensional structure that is complementary. Therefore, complete and rapid prediction of the conformational spa...

    Authors: Sandeepkumar Kothiwale, Jeffrey L. Mendenhall and Jens Meiler

    Citation: Journal of Cheminformatics 2015 7:47

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  35. Content type: Research article

    Predictive regression models can be created with many different modelling approaches. Choices need to be made for data set splitting, cross-validation methods, specific regression parameters and best model cr...

    Authors: Georgia Tsiliki, Cristian R. Munteanu, Jose A. Seoane, Carlos Fernandez-Lozano, Haralambos Sarimveis and Egon L. Willighagen

    Citation: Journal of Cheminformatics 2015 7:46

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  36. Content type: Software

    In silico predictive models have proved to be valuable for the optimisation of compound potency, selectivity and safety profiles in the drug discovery process.

    Authors: Daniel S Murrell, Isidro Cortes-Ciriano, Gerard J P van Westen, Ian P Stott, Andreas Bender, Thérèse E Malliavin and Robert C Glen

    Citation: Journal of Cheminformatics 2015 7:45

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  37. Content type: Database

    In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on tho...

    Authors: James G Jeffryes, Ricardo L Colastani, Mona Elbadawi-Sidhu, Tobias Kind, Thomas D Niehaus, Linda J Broadbelt, Andrew D Hanson, Oliver Fiehn, Keith E J Tyo and Christopher S Henry

    Citation: Journal of Cheminformatics 2015 7:44

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  38. Content type: Research article

    The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and ...

    Authors: Matthew J Harvey, Nicholas J Mason, Andrew McLean, Peter Murray-Rust, Henry S Rzepa and James J P Stewart

    Citation: Journal of Cheminformatics 2015 7:43

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  39. Content type: Research article

    With the rapid increase of the structural data of biomolecular complexes, novel structural analysis methods have to be devised with high-throughput capacity to handle immense data input and to construct massiv...

    Authors: Mohammad ElGamacy and Luc Van Meervelt

    Citation: Journal of Cheminformatics 2015 7:42

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  40. Content type: Research article

    Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure se...

    Authors: Volker D Hähnke, Evan E Bolton and Stephen H Bryant

    Citation: Journal of Cheminformatics 2015 7:41

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  41. Content type: Software

    The design of QSAR/QSPR models is a challenging problem, where the selection of the most relevant descriptors constitutes a key step of the process. Several feature selection methods that address this step are...

    Authors: María Jimena Martínez, Ignacio Ponzoni, Mónica F Díaz, Gustavo E Vazquez and Axel J Soto

    Citation: Journal of Cheminformatics 2015 7:39

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