- Open Access
Molecular structure input on the web
© Ertl; licensee BioMed Central Ltd. 2010
Received: 2 December 2009
Accepted: 2 February 2010
Published: 2 February 2010
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.
A program for the input and editing of molecules is an indispensable part of every cheminformatics or molecular processing system. Such a program is known as a molecule editor, molecular editor or structure sketcher. Its function is to facilitate entry of molecules or reactions into an computer with help of mouse and keyboard actions. There are two types of molecule editors: 3D editors, supporting creation of 3D molecular structures, mainly for use in molecular modeling applications, and 2D editors generating "flat" 2D molecule representations used as input to various molecular processing services, such as searches of chemical databases or the creation of chemical illustrations.
In this overview only 2D molecule editors used for chemical structure input on the web will be covered. The World Wide Web, introduced originally as a medium for exchange of scientific information, is affecting now practically all aspects of our life, but scientific and technical applications still benefit proportionally more from the web technology. Scientific computing is moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet, and the web browser becoming the universal scientific user interface. Chemistry is no exception from this trend and input of molecular structures directly within a web browser is therefore of utmost importance.
Early web-based structure input tools
In the following section the JME Molecule Editor will be described in more details, as a representative example of this type of web-based structure input tools.
JME Molecule Editor
The JME applet is written in Java 1.0, the initial version of Java programming language. Java 1.0 does not support any sophisticated graphics or user interface elements, but on the other side, it is available in all types and versions of web browsers, therefore JME can run practically everywhere, without the need to rely on additional Java plugins (which are not always available). Another advantage of the simple architecture is the JME size (below 40 kB), which assures very fast loading in web pages. Thank to the Java platform independence, the JME runs on Windows PCs, Mac/OS machines and practically all UNIX clones, including, of course, LINUX.
The number of Internet sites which use the JME applet as a molecule input tool is too large to be listed here. These sites include molecular databases, property prediction services, various cheminformatics tools (such as generation of 3D structures, prediction of metabolic sites, combinatorial library design, or QSAR services just to name some) or interactive sites focused on chemistry education. Several such representative applications, which may be of general interest, have been collected here . For an additional review of free web tools focused on applications in medicinal chemistry and drug discovery, see review .
For non-commercial purposes, the JME Editor may be obtained directly from the author of this review.
Server Side Editors
Future of the Molecule Editing on the Web
Another technology for adding interactivity to web pages is Adobe Flash. Although currently used mostly for creating advertisements and video-streamimg applications, integrated scripting language called ActionScript also allows interactive drawing within web pages. To the authors knowledge, no molecule editor has been written in Flash, yet, but available chemical applications like chemical structure viewer , or crystal viewer , show that that Flash can be used to create nice interactive chemical applications. One can therefore expect that sooner or later, a molecule editor written in Flash will appear.
This short overview of history and current status of web-based structure input tools illustrates clearly that the web technology is evolving extremely quickly. New technologies, new tools and services are appearing almost daily. Web-based cheminformatics applications are following this trend. It is also gratifying to see the advent of open source movement in cheminformatics on the Internet, as advocated for example by the Blue Obelisk Group  and witnessed by collaborative projects like Chemistry Development Kit CDK , Jmol , Bioclipse  and several others. In this respect, cheminformatics seems to be closing the gap on the traditionally more open source world of bioinformatics. The future of cheminformatics, and particularly of cheminformatics applications on the web, is indeed exciting.
I want to thank Richard Lewis for critically reading the manuscript and for helpful comments.
- Gasteiger J, Engel T, (Eds): Chemoinformatics - A Textbook. 2003, Wiley-VCH, Weinheim, 137-155.Google Scholar
- Gunda TE: Review of Chemical Drawing Programs. [http://dragon.klte.hu/~gundat/rajzprogramok/dprog.html]
- Weininger D: SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci. 1988, 28: 31-36. 10.1021/ci00057a005.View ArticleGoogle Scholar
- Dundee PRODRG2 Server. [http://davapc1.bioch.dundee.ac.uk/prodrg/]
- Ertl P, Jacob O: WWW-based chemical information system. J Mol Struct (Theochem). 1997, 419: 113-120. 10.1016/S0166-1280(97)00179-6.View ArticleGoogle Scholar
- Daylight GRINS Editor. [http://www.daylight.com/daycgi/grins]
- Molecule Editor_1_0. [http://www.ccl.net/cca/software/SOURCES/JAVA/MoleculeEditor/MoleculeEditor_1_0.java.html]
- ACD/Structure Drawing Applet. [http://www.acdlabs.com/products/java/sda/]
- ChemWriter. [http://chemwriter.com/]
- Edit2D. [http://esc.syrres.com/pointer/default.asp]
- ensochemEditor. [http://www.enso-software.com/WebSite2005/]
- ICedit. [http://infochem.de/products/software/icedit.shtml]
- JavaGrins. [http://www.daylight.com/meetings/emug99/Bharadwaj/SMARTS/]
- JME Molecule Editor. [http://www.molinspiration.com/jme/index.html]
- JUME Molecule Editor. [http://www.upstream.ch/products/topnmr_demo.html]
- KegDraw. [http://www.genome.jp/download/KegDraw/ReadMe-0_1_10Beta.txt]
- MarvinSketch. [http://www.chemaxon.com/marvin/sketch/index.jsp]
- OSIRIS Property Explorer. [http://cheminformatics.ch/propertyExplorer/]
- Symyx JDraw. [http://www.symyx.com/micro/jdraw/demo/JDrawEditorExample.html]
- Krause S, Willighagen E, Steinbeck C: JChemPaint - Using the Collaborative Forces of the: 1 to Develop a Free Editor for 2D Chemical Structures. Molecules. 2000, 5: 93-98. 10.3390/50100093.View ArticleGoogle Scholar
- JMolDraw. [http://sourceforge.net/projects/jmoldraw/]
- MCDL Editor. [http://sourceforge.net/projects/mcdl/]
- SketchEl. [http://sourceforge.net/projects/sketchel/]
- Ertl P, Muehlbacher J, Rohde B, Selzer P: Web-based cheminformatics and molecular property prediction tools supporting drug design and development at Novartis. SAR QSAR Env Res. 2003, 14: 321-328. 10.1080/10629360310001673917.View ArticleGoogle Scholar
- SMARTS - A Language for Describing Molecular Patterns. [http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html]
- Enhanced NCI Database Browser, choose option Substructure and/or 3D Search. [http://cactvs.nci.nih.gov/ncidb2/]
- SMIRKS - A Reaction Transform Language. [http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html]
- Ertl P, Rohde B, Selzer P: Fast calculation of molecular polar surface area directly from SMILES. Daylight European User Meetting, Cambridge, UK. 2000, [http://www.daylight.com/meetings/emug00/Ertl/index.html]Google Scholar
- Interesting cheminformatics tools using the JME Editor. [http://peter-ertl.com/sites-using-jme-editor.html]
- Ertl P, Jelfs S: Designing Drugs on the Internet? Free Web Tools and Services Supporting Medicinal Chemistry. Curr Top Med Chem. 2007, 7: 1491-1501. 10.2174/156802607782194707.View ArticleGoogle Scholar
- Ihlenfeld W-D, Bolton EB, Bryant SH: The PubChem Chemical Structure Sketcher. J Cheminf. 2009, 1: 20-10.1186/1758-2946-1-20.View ArticleGoogle Scholar
- The PubChem Project. [http://pubchem.ncbi.nlm.nih.gov/]
- Molinspiration WebME Editor. [http://www.molinspiration.com/docu/webme/]
- jsMolEditor. [https://github.com/chemhack/jsmoleditor/]
- WebCME Editor. [http://pc.ardoino.com/pj-kem-molecular-editor/]
- ChemDoodle Web Components. [http://web.chemdoodle.com/]
- Flash Chemical 3D Structure Viewer. [http://www.javac.jp/flash/molecular/moleculardraw003/index.html]
- 3D Crystal Viewer. [http://www.dawgsdk.org/crystal/]
- The Blue Obelisk. [http://blueobelisk.sourceforge.net/wiki/Main_Page]
- The Chemistry Deveopment Kit (CDK). [http://sourceforge.net/apps/mediawiki/cdk/index.php?title=Main_Page]
- Jmol. [http://jmol.sourceforge.net/]
- Bioclipse. [http://www.bioclipse.net/]
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.