Skip to content

Advertisement

Articles

Page 4 of 19

  1. 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

    Published on:

  2. 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

    Published on:

  3. 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

    Published on:

  4. 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

    Published on:

  5. 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

    Published on:

  6. 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

    Published on:

  7. 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

    Published on:

  8. 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

    Published on:

  9. 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

    Published on:

  10. 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

    Published on:

  11. 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

    Published on:

  12. 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

    Published on:

  13. 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

    Published on:

  14. 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

    Published on:

  15. 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

    Published on:

  16. 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

    Published on:

  17. 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

    Published on:

  18. 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

    Published on:

  19. 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

    Published on:

  20. 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

    Published on:

  21. 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

    Published on:

  22. 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

    Published on:

  23. 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

    Published on:

  24. 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

    Published on:

  25. 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

    Published on:

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

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

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

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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

    Published on:

  34. 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

    Published on:

  35. 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

    Published on:

  36. 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

    Published on:

  37. 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

    Published on:

  38. 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

    Published on:

  39. 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

    Published on:

  40. 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

    Published on:

2017 Journal Metrics

  • Speed
    80 days from submission to first decision
    136 days from submission to acceptance
    15.7 days from acceptance to publication

    Usage 
    362,935 downloads
    977 Altmetric mentions

Advertisement