MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations. It also produces output files that can be used in Raster3d.

molsKetch is a molecular drawing tool for 2D molecular structures. Its goal is to help you draw molecules quick and easily. As well as allowing the user to export high quality images in a number of vector and bitmap formats, it can read and write multiple chemical file formats (using the Open Babel library). molsKetch features intelligent addition/removal of hydrogen atoms and a built-in library that provides quick access to regularly used molecules and functional groups.

MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structure. MolSurfer can be used to study protein-protein and protein-DNA/RNA interfaces.

MOPAC is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. The semi-empirical Hamiltonians MNDO, MINDO/3, AM1, and PM3 are used in the electronic part of the calculation to obtain molecular orbitals, the heat of formation and its derivative with resperivative with respect to molecular geometry.

MOPAC2007 is a general-purpose semiempirical quantum mechanics package for the study of chemical properties and reactions in gas, solution, or solid-state. MOPAC2007 can be used to directly predict numerous chemical and physical properties, such as Gibbs free energies, activation energies, reaction paths, dipole moments, non-linear optical properties, and infrared spectra. It is based on the public domain MOPAC 7.

MOSCITO is designed for molecular dynamics simulations of condensed phase systems defined by classical molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS.

Moveiemol is a program for visualization and animation of molecular structures. Moviemol typically takes sets of molecular coordinates and displays each of these sets or frames one after the other to create a movie. The molecules/atoms/ions are displayed in ball-and-stick form. At any moment during the animation, the molecules can be rotated or translated, magnified or diminished. The program also produces very nice postscript images of publication quality.

MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. It runs on a wide range of architectures ranging from individual workstations to symmetric multiprocessors to massively parallel computers. Its design is object oriented, using the C++ programming language.

MSMS stands for Michel Sanner's Molecular Surface, or Maximal Speed Molecular Surface. It allows the user to compute very efficiently triangulations of solvent excluded surfaces.

MULTIMODE performs Vibrational Self Consistent Field (VSCF) and several types of "CI" calculations for the rovibrational energies and wavefunctions of polyatomic molecules, transition states, clusters, etc. The code is based on the Watson Hamiltonian for non-linear molecules.