Molecular structure input on the web

By Peter Ertl. 2010

103 citations recorded by the source corpus.

A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

Subfields: Computational Theory and Mathematics, Environmental Chemistry, Physical and Theoretical Chemistry

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Citations in the corpus

ChEMBL: a large-scale bioactivity database for drug discovery (2011, background): “The interface provides a choice of several different drawing tools (26), allowing users to sketch in a structure or substructure of interest (Figure 1).”
CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures (2011, methodology): “SMILES is bridging the opposite ends of humanfriendly molecular drawings, achieved with molecule editors [12,13], and computer-friendly connection tables (matrices), both used in representing molecular structures.”
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information (2011, methodology): “For chemistry-related features we used the JME molecule editor [17], the CDK toolkits [81] and the ChemAxon (http://www.”