A molecule editor is a computer program for creating and modifying representations of chemical structures. There are a number types of molecule editor. Molecular drawing programs are used to generate two-dimensional (flat) representations of molecules and chemical reactions that can be used as illustrations or for querying chemical databases. Three-dimensional molecule editors are used to build molecular models, usually as part of molecular modelling software packages. Database molecular editors such as Leatherface[1], RECAP[2] and Molecule Slicer [3] allow large numbers of molecules to be modified automatically according to rules such as 'deprotonate carboxylic acids' or 'break exocyclic bonds' that can be specified by the user.
Most molecule editors use proprietary file formats, but most can read and write several file formats, including SMILES, a short ASCII-representation of molecules.
Files generated by two- or three-dimensional molecule editors can also be displayed by molecular graphics tools, which can be realized as a small applet to show molecules in web pages.
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Standalone programs
- ACD/ChemSketch: proprietary software from ACD/Labs, both in commercial and freeware versions. Available only for Windows.
- Ascalaph Designer: proprietary software, both in commercial and freeware versions. Available for Windows.
- Bioclipse: open source software, EPL + a GPL-exception, Java. Eclipse RCP based.
- BKchem: open source software, GPL, Python. Largely platform-independent.
- ChemDoodle: proprietary software from iChemLabs. Available for Windows, Mac, and Linux.
- ChemDraw: proprietary software from CambridgeSoft. Available for Windows and Mac.
- ICEDIT: proprietary software from InfoChem.
- ChemTool: free software for drawing chemical structural formulas, written in C using GTK for Unix and Linux.
- ISIS/Draw and Symyx Draw: proprietary software from MDL Information Systems and Symyx Technologies.
- JChemPaint: open source software, LGPL, Java.
- MarvinSketch/View: proprietary software from ChemAxon, both in commercial and freeware versions (see terms). Chemical editor and viewer, desktop version (Java Beans).
- MarvinSpace: proprietary software from ChemAxon, both in commercial and freeware versions (see terms). 3D macromolecular visualization and ligand editing, desktop version (Java Beans).
- molsKetch: open source, GPL, multiplatform editor, based on Qt4.
- XDrawChem: open source software, GPL, C++, based on OpenBabel. Available for Windows, Linux, Mac OS X.
Applets
- JChemPaint: open source software, LGPL, Java. Both editor and viewer applets.
- JME Molecular Editor by Peter Ertl, available from Molinspiration. Freeware for noncommercial use. Java.
- MarvinSketch: proprietary software from ChemAxon, both in commercial and freeware versions (see terms). Chemical editor applet implementation.
- MarvinSpace: proprietary software from ChemAxon, both in commercial and freeware versions (see terms). 3D macromolecular visualization and ligand editing.
- SDA, ACD/Structure Drawing Applet: proprietary software from ACD/Labs, both in commercial and freeware versions.
Online editors
- Marvin molecule editor and viewer: proprietary software from ChemAxon. Supports all major formats and structure/query features. This Java implementation also includes unlimited structure based predictions for a range of properties (pKa, logD, name<>structure, etc.).
- Molinspiration WebME molecule editor: proprietary software, based on Web 2.0 and Ajax technology which does not require Java.
- PubChem online molecule editor, supports SMILES, SMARTS and InChI as well as all common chemical file formats.
- jsMolEditor, the world's first molecule structure editor in Javascript. Runs in most web browsers, no plugin or virtual machine is required.
See also
- Molecular modelling
- Molecular graphics
- Chemical databases
- PubChem
- ChemSpider
- Software for molecular mechanics modeling
- Molecular Design software
References
- ^ Kenny, P.W.; Sadowski, J. (2005) Structure modification in chemical databases Chemoinformatics in drug discovery (editor—Oprea, T.I.), 271-285 (Wiley).
- ^ Lewell, X.Q.; Judd, D.B; Watson, S.P.; Hann, M.M. (1998) RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry J. Chem. Inf. Comput. Sci. 38, 511-522.
- ^ Vieth, M.; Siegel, M.G.; Higgs, R.E.; Watson, I.A.; Robertson, D.H.; Savin, K.A.; Durst, G.L.; Hipskind; P.A. (2004) Characteristic Physical Properties and Structural Fragments of Marketed Oral Drugs J. Med. Chem. 47, 224-232.
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