JSME: a free molecule editor in JavaScript

Bienfait, Bruno; Ertl, Peter

doi:10.1186/1758-2946-5-24

Cited by 261 publications

(209 citation statements)

References 3 publications

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“…Some other JavaScript molecular viewers specialize in small molecules, allowing users to build and edit molecules online [13,14,52,53]. Probably the most widely used, free tool for small molecules is JSME [13], the JavaScript version of the Java-based molecular builder and editor JME.…”

Section: Javascript Molecular Viewers Editors and Calculators Frommentioning

confidence: 99%

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Web Apps Come of Age for Molecular Sciences

Abriata

2017

Informatics

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Whereas server-side programs are essential to maintain databases and run data analysis pipelines and simulations, client-side web-based computing tools are also important as they allow users to access, visualize and analyze the content delivered to their devices on-the-fly and interactively. This article reviews the best-established tools for in-browser plugin-less programming, including JavaScript as used in HTML5 as well as related web technologies. Through examples based on JavaScript libraries, web applets, and even full web apps, either alone or coupled to each other, the article puts on the spotlight the potential of these technologies for carrying out numerical calculations, text processing and mining, retrieval and analysis of data through queries to online databases and web services, effective visualization of data including 3D visualization and even virtual and augmented reality; all of them in the browser at relatively low programming effort, with applications in cheminformatics, structural biology, biophysics, and genomics, among other molecular sciences.

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Section: Javascript Molecular Viewers Editors and Calculators Frommentioning

confidence: 99%

“…Most work as embeddable libraries but are also available as full web apps. JSME [13] A library to create and edit small molecules graphically, often used as the starting point for subsequent calculations or database queries. CH5M3D [14], Chemozart [15] Libraries to edit molecules in 3D.…”

Section: Molecular Visualization and Editingmentioning

confidence: 99%

Web Apps Come of Age for Molecular Sciences

Abriata

2017

Informatics

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“…65 Willing to provide predictive and interpretative tools for toxicity prediction, we have been working to implement highly predictive QSAR models in web and mobile apps with intuitive usage and interpretation. Both Pred-hERG and Pred-Skin allows the user to make predictions by pasting SMILES strings or drawing molecules in the JSME 66 molecule editor. Alternatively, the user can load .sdf or .mol files.…”

Section: Usage and Interpretation Of Apps For Toxicity Predictionmentioning

confidence: 99%

Development of Web and Mobile Applications for Chemical Toxicity Prediction

Alves¹,

Braga²,

Muratov³

et al. 2018

J. Braz. Chem. Soc.

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Computational tools are recognized to provide high-quality predictions for the assessment of chemical toxicity. In the recent years, mobile devices have become ubiquitous, allowing for the development of innovative and useful models implemented as chemical software applications. Here, we will briefly discuss this recent uptick in the development of web-based and mobile applications for chemical problems, focusing on best practices, development, usage and interpretation. As an example, we also describe two innovative apps (Pred-hERG and Pred-Skin) for chemical toxicity prediction developed in our laboratory. These applications are based on predictive quantitative structure-activity relationships (QSAR) models developed using the largest publicly available datasets of structurally diverse compounds. The developed tools ensure both highly accurate predictions and easy interpretation of the models, allowing users to discriminate potential toxicants and to purpose structural modifications to design safer chemicals.

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“…Spice compounds may be searched using a range of molecular features such as its common name, MeSH ID, IUPAC name, PubChem ID, molecular weight, hydrogen bond donors/acceptors or molecular hydrophobicity (AlogP), apart from drawing their structure (JSME Molecular Editor (Bienfait and Ertl, 2013)). For instance, the users can search with common name 'bisabolol', MeSH ID, 'C004497', PubChem ID, '10586', IUPAC name, '6-methyl-2-(4-methylcyclohex-3-en-1-yl)hept-5-en-2-ol', Canonical SMILES, 'CC1=CCC(CC1)C(C)(CCC=C(C)C)O', Molecular Formula, 'C16H24O10' or its Isomeric SMILES, 'CC1=CCC(CC1)C(C)(CCC=C(C)C)O'.…”

Section: Searching In Spicerxmentioning

confidence: 99%

“…and PostgreSQL (https://www.postgresql.org/). The frontend was built using HTML, CSS, JavaScript, AJAX, jQuery, JSME Molecular Editor (Bienfait and Ertl, 2013), Bootstrap, Jmol, DataTables and Google Charts. An Apache HTTP Server has been used to route requests to the Django application and to enable data compression for faster page load times.…”

Section: Webserver Tech Stackmentioning

confidence: 99%

SpiceRx: an integrated resource for the health impacts of culinary spices and herbs

Tuwani

Garg

et al. 2018

Preprint

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Spices and herbs are key dietary ingredients used in cuisines across the world. They have been reported to be of medicinal value for a wide variety of diseases through a large body of biomedical investigations. Bioactive phytochemicals in these plant products form the basis of their therapeutic potential as well as adverse effects. A systematic compilation of empirical data involving these aspects of culinary spices and herbs could help unravel molecular mechanisms underlying their effects on health.SpiceRx provides a platform for exploring the health impact of spices and herbs used in food preparations through a structured database of tripartite relationships with their phytochemicals and disease associations. Starting with an extensive dictionary of culinary spices and herbs, their disease associations were text mined from MEDLINE, the largest database of biomedical abstracts, assisted with manual curation. This information was further combined with spice-phytochemical and phytochemical-disease associations. SpiceRx is an integrated repertoire of evidence-based knowledge pertaining to the health impacts of culinary spices and herbs, and facilitates their disease-specific culinary recommendations as well as exploration of molecular mechanisms underlying their health effects. Availability and Implementation:SpiceRx is available at http://cosylab.iiitd.edu.in/spicerx and supports all modern browsers. SpiceRx is implemented with Python web development framework Django and relational database PostgreSQL; the front-end was built using HTML, CSS,

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JSME: a free molecule editor in JavaScript

Cited by 261 publications

References 3 publications

Web Apps Come of Age for Molecular Sciences

Web Apps Come of Age for Molecular Sciences

Development of Web and Mobile Applications for Chemical Toxicity Prediction

SpiceRx: an integrated resource for the health impacts of culinary spices and herbs

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