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Afferent - Tools for tracking the information associated with combinatorial libraries and parallel medicinal chemistry syntheses.
Automatic Organic Chemical Reactions - A program based on a mathematical representation of organic synthesis that generates all products of a synthesis on an input of organic compounds.
Building the Shortest Synthesis Route - This article, published in CHEMTECH in 1998, is a nice introduction to the field of Computer-Assisted Organic Synthesis.
CAChe Group - Provides software to view and predict 3D molecular structure and properties and to analyze the relationship between structure and properties or structure and reactivity. CAChe is a tool for medicinal, polymer, process and synthetic chemists.
ChemNomParse Project - An open source project to create an IUPAC nomenclature parser.
Organic Synthesis Exploration Tool - Free software for computer-assisted organic synthesis, intended mainly for use in education. Applet-based. Source code available.
SynGen - A program for automatic synthesis generation which focuses on the shortest, most economical routes. Uses a generalized model of organic reactions and functionality to simplify the problem space. Macintosh beta version available for download.
Systematichem - Computational organic chemistry software for retrosynthesis and synthesis development.
TORVS Research Team - Software for reaction prediction, synthesis design, classification of organic reactions, chemical information, calculation of 3D coordinates, and calculation of physicochemical parameters.