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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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

  15. 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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  16. 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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  17. 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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  18. 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

  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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