achemso is a package which formats the Bibliography according to the standards of the American Chemical Society; includes (after installation) the needed BibTeX style file.
ChemTeX is a collection of macros to assist in writing chemical documents in TeX/LaTeX.
Chemical Markup Language is an XML application for storing and transporting chemical information. CML (Chemical Markup Language) is a new approach to managing molecular information using recently developed Internet tools such as XML and Java. It is based strictly on SGML, the most robust and widely used system for precise information management in many areas. It has been developed over several years and has been tested in many areas and on a variety of machines.
DMax Chemistry Assistant
(commercial) DMax Chemistry Assistant automatically finds, formulates and shows scientific hypotheses that best match your observations. The hypotheses are automatically validated on a separate test set, and can be collectively applied to unseen compounds for virtual screening.
(commercial) Dragon is an application for the calculation of molecular descriptors. These descriptors can be used to evaluate molecular structure-activity or structure-property relationships, as well as for similarity analysis and high-throughput screening of molecule databases.
kfile_chemical is a set of kfile plugins for chemistry documents. It has support for XYZ, PDB, MDL mol/sd, Mol2, CML, ShelX, SMILES and CIF files.
MGLTools is a suite of software including PMV (Python Molecular Viewer), a molecule viewing and manipulation environment, ADT (AutoDockTools) for looking at AutoDock results, and pyBabel, a Python re-implementation of some of the features of Babel v1.6.
(commercial) MOE (Molecular Operating Environment) can be used to manipulate and analyse large collections of compounds in a spreadsheet-like environment. It can be used to calculate descriptors, for building QSAR/QSPR models, for similarity searching and diverse subset selection, conformational searching and 3D pharmacophore searching.
MolCart allows you to handle very large libraries of chemical compounds. Moreover, it uses a fast relational database which is freely available without any limitations. Molcart is also unrestricted in terms of number of users.
(commercial) QikProp provides rapid predictions for physically-significant descriptors and pharmaceutically-relevant properties of neutral organic molecules.
(commercial) VolSurf is a computational procedure to produce 2D molecular descriptors from 3D molecular interaction energy grid maps. The basic idea of VolSurf is to compress the information present in 3D maps into a few 2D numerical descriptors which are very simple to understand and to interpret. VolSurf descriptors are specifically designed for the optimisation of in silico pharmacokinetic properties (eADME or IS-DMPK).
WODCA is a computer program for the interactive planning of organic syntheses. It has been developed during the last ten years and further development is currently in progress. The target user group of WODCA are organic chemists in research and development working on synthesis problems.
XCombust is a utility for elementary analysis data.
xem is a simple software simulating titration for various systems.