Orbdraw is a visualization program for displaying molecular orbital and electron density data from Gaussian, Gamess, Jaguar, Hondo, Mopac or Ampac calculations. Orbdraw can display the molecular orbitals, electron densities or spin densities in 3D as either wire frames or solid surfaces and can map orbitals or charges onto the density surfaces.

The program ORCA is a modern electronic structure program package with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to correlated ab initio methods. It can also treat environmental and relativistic effects.

ORTEP (Oak Ridge Thermal Ellipsoid Plot) is a program for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoin probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. There is also a Linux-specific <a href=http://ruby.chemie.uni-freiburg.de/~martin/ortep/ortep.html>Linux ORTEP page</a>.

OS-ELN (Open Source Electronic Lab Notebook) will be of particular interest to Universities and Colleges needing a simple, low-cost ELN to be used by their students in classes. The system is easily and cost effectively deployed, and can be expanded and modified as needed.

OSET (Organic Synthesis Exploration Tool) is a computer-assisted organic synthesis (CAOS) program for the retrosynthetic analysis of target molecules. Intended for educational use, as a tool for learning chemical synthetic design at undergraduate organic chemistry courses.

OVITO (Open Visualization Tool) allows the analysis and visualization of large-scale atomistic datasets produced by molecular dynamics/statics and Monte-Carlo simulation codes.

Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

PaDEL-Descriptor is a GUI for calculating molecular descriptors and fingerprints. The software currently calculates 856 descriptors (722 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints. The descriptors and fingerprints are calculated using the Chemistry Development Kit with some additional descriptors and fingerprints. These additions include atom type electrotopological state descriptors, extended topochemical atom (ETA) descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth.

The Pallas suite includes software for predicting pKa (pKalc), logP (PrologP), logD (PrologD), toxicity values (HazardExprt) and metabolitic fate (MetabolExpert) based on structural formula of compounds.

Pcmodel is a molecular modeling package with interfaces to many quantum chemistry packages. It also includes support for geometry optimisation with various force fields as well as conformational searching.