Molecule editor
From Wikipedia, the free encyclopedia
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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[edit] Molecule editors
[edit] Standalone programs
- AGM Build
- ACD/ChemSketch (ACD/Labs), also available as freeware.
- Ascalaph Designer
- ChemDraw
- ISIS Draw (MDL)
- BKchem: Open Source, GPL, Python.
- Smormoed: Open Source, modified BSD license, C programming language. Available for Linux, FreeBSD, Mac OS X
- JChemPaint (JCP): Open Source, LGPL Java. Based on the Chemistry Development Kit (CDK).
- XDrawChem: Open Source, GPL, C++. Based on OpenBabel. Available for Windows, Linux, Mac OS X
- ChemTool, free software editor
- ChemAxon's MarvinSketch/View: chemical editor and viewer - desktop version (Java Beans). ::Free on your desktop.
- ChemAxon's MarvinSpace: 3D macromolecular visualization and ligand editing - desktop version (Java Beans). ::Free on your desktop.
- molsKetch: Open Source, GPL, multiplatform (Qt4-based) editor
[edit] Applets
- SDA from ACD/Labs
- JME from molinspiration
- ChemAxon's MarvinSketch: chemical editor Java Applet implementation. ::Free for free web pages. ::Free on your desktop.
- ChemAxon's MarvinSpace: 3D macromolecular visualization and ligand editing. ::Free for free web pages. :: Free on your desktop.
- JChemPaint: Open Source, LGPL Java, demo.
[edit] Online editors
- PubChem online molecule editor, supports SMILES/SMARTS and InChI as well as all common chemical file formats.
- Marvin Molecule editor and Viewer. Supports all major formats and structure/query features. This implementation also includes unlimited structure based predictions for a range of properties (pKa, logD etc)
- Molinspiration WebME molecule editor based on Web2.0 and Ajax technology which does not require Java
[edit] See also
- Molecular modelling
- Molecular graphics
- Chemical databases
- PubChem
- ChemSpider
- Software for molecular mechanics modeling
[edit] 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.
