The free JME Molecular Editor is a Java applet which allows easy creation and editing of organic molecules and reactions directly within web page, and creation of molecule SMILES or Molfile
A molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. [FAQ]
Jmol is an open-source java viewer for chemical structures in 3D, it is fully functional in most browsers.[tutorial]
Introduction to computational modelling methods used nowadays as standard tools by organic chemists for searching for, rationalising and predicting structure and reactivity of organic, bio-organic and organometallic molecules.
This list concentrates on programs for which the source code is available in some form.
WWW software for drawing a molecular structure, running calculations (Gaussian, MOPAC and GAMESS supported) and visualization/manipulation of the results.
Program to convert, manage andvisualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs)
Free interactive calculation of molecular properties (including logP, polar surface area and other useful descriptors) and calculation of drug-likeness score for GPCR ligands, ion channel modulators and kinase inhibitors.