ChemDoodle!

ACD/ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. Use it to produce professional looking structures and diagrams for reports and publications.

Communicate with the natural language of chemical structures, biological pathways, and models

Marvin is a great alternative to the subscription based ChemDraw by CambridgeSoft. It is a collection of tools for drawing, displaying and characterizing chemical structures, substructures and reactions.It will also convert structures you create to various molecular visualiztion formats, such as .pdb and .mol, compatible with programs such as PyMOL and SwissPDB Viewer.

BKChem is a free (as in free software :o) chemical drawing program. It was conceived and written by Beda Kosata and is currently maintained by Reinis Danne.

JChemPaint is an editor and viewer for chemical structures in 2D. It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems. There is a standalone application (editor), and two varieties of applet (editor and viewer) that can be integrated into web pages.JChemPaint is currently being developed as part of The Chemistry Development Kit, and a Standard Widget Toolkit-based JChemPaint application is being developed, as part of Bioclipse.External links JChemPaint page The Chemistry Development Kit »