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

  14. 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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  15. 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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  16. 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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  17. 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

  18. 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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  19. 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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Page 6 of 35

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