MEXICO simulates the NMR lineshapes of coupled spin systems undergoing chemical exchange. It will simulate systems and, if experimental data are available, it will perform an iterative fit to give optimized values of the parameters.

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.

Mindy is a very simple, serial molecular dynamics program derived from NAMD source code. It currently uses xplor parameter and structure files.

MMC is a Metropolis Monte Carlo program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, extension-biased and local torsion changes, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change).

MMTK (the Molecular Modelling Toolkit) is a program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations.

Mnova Suite is a GUI with plugins for processing and reporting NMR data, predicting NMR data and processing MS data. Individual plugins are available separately.

ModelFree is a program for optimizing Lipari-Szabo model free parameters to heteronuclear NMR spin relaxation data.

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. It has an embedded scripting language, SVL (Scientific Vector Language).

Mol_Volume calculates the volume of a macromolecule by a method somewhat akin to the Monte Carlo method, namely, by measuring how many vertices of a dense regular grid happen to be within the probe radius of the molecule's atoms.

Includes POLARIS and ENZYMIX in a unique package with an interface. Enzymix is a macromolecular simulation program designed to study the functions of proteins. Polaris is a fast converging computational software based on the Protein Dipoles - Langevin Dipoles (PDLD) approach.