Journal of Cheminformatics

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		Book report Review of “Contemporary computer-assisted approaches to molecular structure elucidation (new developments in NMR)” by Mikhail E Elyashberg, Antony Williams and Kirill Blinov Christoph Steinbeck Journal of Cheminformatics 2013, 5:29 (3 June 2013) Abstract \| Full text \| PDF \| ePUB
		Database HIM-herbal ingredients in-vivo metabolism database Hong Kang, Kailin Tang, Qi Liu, Yi Sun, Qi Huang, Ruixin Zhu, Jun Gao, Duanfeng Zhang, Chenggang Huang, Zhiwei Cao Journal of Cheminformatics 2013, 5:28 (31 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Defining a novel k-nearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions Faizan Sahigara, Davide Ballabio, Roberto Todeschini, Viviana Consonni Journal of Cheminformatics 2013, 5:27 (30 May 2013) Abstract \| Full text \| PDF \| PubMed
		Research article Open-source platform to benchmark fingerprints for ligand-based virtual screening Sereina Riniker, Gregory A Landrum Journal of Cheminformatics 2013, 5:26 (30 May 2013) Abstract \| Provisional PDF \| PubMed \| Graphical abstract
		Research article From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language Wibe A de Jong, Andrew M Walker, Marcus D Hanwell Journal of Cheminformatics 2013, 5:25 (24 May 2013) Abstract \| Provisional PDF \| PubMed \| Graphical abstract
		Software JSME: a free molecule editor in JavaScript Bruno Bienfait, Peter Ertl Journal of Cheminformatics 2013, 5:24 (21 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary \| Graphical abstract A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface.
		Methodology The ChEMBL database as linked open data Egon L Willighagen, Andra Waagmeester, Ola Spjuth, Peter Ansell, Antony J Williams, Valery Tkachenko, Janna Hastings, Bin Chen, David J Wild Journal of Cheminformatics 2013, 5:23 (8 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary \| Graphical abstract An ongoing project converting data from the ChEMBL database into RDF triples. The ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications.
		Research article In-silico design of computational nucleic acids for molecular information processing Effirul Ramlan, Klaus-Peter Zauner Journal of Cheminformatics 2013, 5:22 (7 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding Ying-Ting Lin Journal of Cheminformatics 2013, 5:21 (30 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Graphical abstract
		Software Extracting and connecting chemical structures from text sources using chemicalize.org Christopher Southan, Andras Stracz Journal of Cheminformatics 2013, 5:20 (23 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary \| Graphical abstract This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and databases, including structure searches in PubChem, InChIKey searches in Google and the chemicalize.org archive
		Research article Druggable chemical space and enumerative combinatorics Melvin J Yu Journal of Cheminformatics 2013, 5:19 (18 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Graphical abstract
		Research article Predicting p K _avalues from EEM atomic charges Radka Vařeková, Stanislav Geidl, Crina-Maria Ionescu, Ondřej Skřehota, Tomáš Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koča Journal of Cheminformatics 2013, 5:18 (10 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Graphical abstract
		Research article The influence of the inactives subset generation on the performance of machine learning methods Sabina Smusz, Rafał Kurczab, Andrzej J Bojarski Journal of Cheminformatics 2013, 5:17 (5 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Using Pareto points for model identification in predictive toxicology Anna Palczewska, Daniel Neagu, Mick Ridley Journal of Cheminformatics 2013, 5:16 (22 March 2013) Abstract \| Provisional PDF \| PubMed
		Research article Mining basic active structures from a large-scale database Naoto Takada, Norihito Ohmori, Takashi Okada Journal of Cheminformatics 2013, 5:15 (16 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Software Applications of the InChI in cheminformatics with the CDK and Bioclipse Ola Spjuth, Arvid Berg, Samuel Adams, Egon L Willighagen Journal of Cheminformatics 2013, 5:14 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract
		Research article TB Mobile: a mobile app for anti-tuberculosis molecules with known targets Sean Ekins, Alex M Clark, Malabika Sarker Journal of Cheminformatics 2013, 5:13 (6 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Graphical abstract
		Review Computational mass spectrometry for small molecules Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker Journal of Cheminformatics 2013, 5:12 (1 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Database Dragon exploration system on marine sponge compounds interactions Sunil Sagar, Mandeep Kaur, Aleksandar Radovanovic, Vladimir B Bajic Journal of Cheminformatics 2013, 5:11 (16 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A publicly available database is presented where users can explore information, compiled by text- and data-mining approaches, on biological and chemical data related to marine sponge compounds
		Research article Random forests for feature selection in QSPR Models - an application for predicting standard enthalpy of formation of hydrocarbons Ana L Teixeira, João P Leal, Andre O Falcao Journal of Cheminformatics 2013, 5:9 (11 February 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract
		Review InChI in the wild: an assessment of InChIKey searching in Google Christopher Southan Journal of Cheminformatics 2013, 5:10 (11 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Graphical abstract
		Research article New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms Hwanho Choi, Hongsuk Kang, Hwangseo Park Journal of Cheminformatics 2013, 5:8 (4 February 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract
		Review InChI - the worldwide chemical structure identifier standard Stephen Heller, Alan McNaught, Stephen Stein, Dmitrii Tchekhovskoi, Igor Pletnev Journal of Cheminformatics 2013, 5:7 (24 January 2013) Abstract \| Full text \| PDF \| PubMed
		Commentary Chemical datuments as scientific enablers Henry S Rzepa Journal of Cheminformatics 2013, 5:6 (23 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary \| Graphical abstract An attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal is presented, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5.
		Research article Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines Sheng Tian, Youyong Li, Junmei Wang, Xiaojie Xu, Lei Xu, Xiaohong Wang, Lei Chen, Tingjun Hou Journal of Cheminformatics 2013, 5:5 (21 January 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract

	All
		Book report Review of “Contemporary computer-assisted approaches to molecular structure elucidation (new developments in NMR)” by Mikhail E Elyashberg, Antony Williams and Kirill Blinov Christoph Steinbeck Journal of Cheminformatics 2013, 5:29 (3 June 2013) Abstract \| Full text \| PDF \| ePUB
		Database HIM-herbal ingredients in-vivo metabolism database Hong Kang, Kailin Tang, Qi Liu, Yi Sun, Qi Huang, Ruixin Zhu, Jun Gao, Duanfeng Zhang, Chenggang Huang, Zhiwei Cao Journal of Cheminformatics 2013, 5:28 (31 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Defining a novel k-nearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions Faizan Sahigara, Davide Ballabio, Roberto Todeschini, Viviana Consonni Journal of Cheminformatics 2013, 5:27 (30 May 2013) Abstract \| Full text \| PDF \| PubMed
		Research article Open-source platform to benchmark fingerprints for ligand-based virtual screening Sereina Riniker, Gregory A Landrum Journal of Cheminformatics 2013, 5:26 (30 May 2013) Abstract \| Provisional PDF \| PubMed \| Graphical abstract
		Research article From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language Wibe A de Jong, Andrew M Walker, Marcus D Hanwell Journal of Cheminformatics 2013, 5:25 (24 May 2013) Abstract \| Provisional PDF \| PubMed \| Graphical abstract
		Software JSME: a free molecule editor in JavaScript Bruno Bienfait, Peter Ertl Journal of Cheminformatics 2013, 5:24 (21 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary \| Graphical abstract A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface.
		Methodology The ChEMBL database as linked open data Egon L Willighagen, Andra Waagmeester, Ola Spjuth, Peter Ansell, Antony J Williams, Valery Tkachenko, Janna Hastings, Bin Chen, David J Wild Journal of Cheminformatics 2013, 5:23 (8 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary \| Graphical abstract An ongoing project converting data from the ChEMBL database into RDF triples. The ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications.
		Research article In-silico design of computational nucleic acids for molecular information processing Effirul Ramlan, Klaus-Peter Zauner Journal of Cheminformatics 2013, 5:22 (7 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding Ying-Ting Lin Journal of Cheminformatics 2013, 5:21 (30 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Graphical abstract
		Software Extracting and connecting chemical structures from text sources using chemicalize.org Christopher Southan, Andras Stracz Journal of Cheminformatics 2013, 5:20 (23 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary \| Graphical abstract This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and databases, including structure searches in PubChem, InChIKey searches in Google and the chemicalize.org archive
		Research article Druggable chemical space and enumerative combinatorics Melvin J Yu Journal of Cheminformatics 2013, 5:19 (18 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Graphical abstract
		Research article Predicting p K _avalues from EEM atomic charges Radka Vařeková, Stanislav Geidl, Crina-Maria Ionescu, Ondřej Skřehota, Tomáš Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koča Journal of Cheminformatics 2013, 5:18 (10 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Graphical abstract
		Research article The influence of the inactives subset generation on the performance of machine learning methods Sabina Smusz, Rafał Kurczab, Andrzej J Bojarski Journal of Cheminformatics 2013, 5:17 (5 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Using Pareto points for model identification in predictive toxicology Anna Palczewska, Daniel Neagu, Mick Ridley Journal of Cheminformatics 2013, 5:16 (22 March 2013) Abstract \| Provisional PDF \| PubMed
		Research article Mining basic active structures from a large-scale database Naoto Takada, Norihito Ohmori, Takashi Okada Journal of Cheminformatics 2013, 5:15 (16 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Software Applications of the InChI in cheminformatics with the CDK and Bioclipse Ola Spjuth, Arvid Berg, Samuel Adams, Egon L Willighagen Journal of Cheminformatics 2013, 5:14 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract
		Research article TB Mobile: a mobile app for anti-tuberculosis molecules with known targets Sean Ekins, Alex M Clark, Malabika Sarker Journal of Cheminformatics 2013, 5:13 (6 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Graphical abstract
		Review Computational mass spectrometry for small molecules Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker Journal of Cheminformatics 2013, 5:12 (1 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Database Dragon exploration system on marine sponge compounds interactions Sunil Sagar, Mandeep Kaur, Aleksandar Radovanovic, Vladimir B Bajic Journal of Cheminformatics 2013, 5:11 (16 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A publicly available database is presented where users can explore information, compiled by text- and data-mining approaches, on biological and chemical data related to marine sponge compounds
		Research article Random forests for feature selection in QSPR Models - an application for predicting standard enthalpy of formation of hydrocarbons Ana L Teixeira, João P Leal, Andre O Falcao Journal of Cheminformatics 2013, 5:9 (11 February 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract
		Review InChI in the wild: an assessment of InChIKey searching in Google Christopher Southan Journal of Cheminformatics 2013, 5:10 (11 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Graphical abstract
		Research article New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms Hwanho Choi, Hongsuk Kang, Hwangseo Park Journal of Cheminformatics 2013, 5:8 (4 February 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract
		Review InChI - the worldwide chemical structure identifier standard Stephen Heller, Alan McNaught, Stephen Stein, Dmitrii Tchekhovskoi, Igor Pletnev Journal of Cheminformatics 2013, 5:7 (24 January 2013) Abstract \| Full text \| PDF \| PubMed
		Commentary Chemical datuments as scientific enablers Henry S Rzepa Journal of Cheminformatics 2013, 5:6 (23 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary \| Graphical abstract An attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal is presented, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5.
		Research article Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines Sheng Tian, Youyong Li, Junmei Wang, Xiaojie Xu, Lei Xu, Xiaohong Wang, Lei Chen, Tingjun Hou Journal of Cheminformatics 2013, 5:5 (21 January 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract