MOLCAS allows an accurate ab initio treatment of very general electronic structure problems for molecular systems in both ground and excited states. MOLCAS contains a number of codes that can perform such calculations (MP2, CC, CPF, CCSD(T) etc.). It can also treat highly degenerate states using general and effective multiconfigurational SCF calculations at the CASSCF level, as well as RASSCF.
MOLDA for Protein Modeling
MOLDA is a molecular modeling program. 3D molecular structures in VRML and POV-Ray formats can be generated using the output from a variety of computational chemistry programs.
MOLDEN is a package for displaying molecules, electron density, and orbitals from ab initio and semi-empirical packages. It has a powerful Z-matrix editor.
Moldy is a general-purpose molecular dynamics simulation program. It is sufficiently flexible that it ought to be useful for a wide range of simulation calculations of atomic, ionic and molecular systems.
Molegro Molecular Viewer
Molegro Molecular Viewer is a free cross-platform application for visualization of molecules and analysis of protein-ligand interactions.
Molegro Virtual Docker
Molegro Virtual Docker is an integrated platform for predicting protein-ligand interactions. It handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands.
MOLEKEL is an interactive, three-dimensional molecular graphics package. MOLEKEL represents molecules,it can superimpose molecules, calculates and displays isosurfaces of electron and spin densities as well as molecular orbitals from the output of various electronic structure calculation programs. MOLEKEL can animate and display vibrational modes, animate geometry optimizations and multiple coordinate PDB and XYZ files.
Mollie is a small web-oriented database for molecular information. It uses Perl for CGI, and PostgreSQL.
MOLMOL is a program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
Molpro is a system of ab initio programs for molecular electronic structure calculations. with an emphasis on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. Using recently developed integral-direct local electron correlation methods, accurate ab initio calculations can be performed for much larger molecules than with most other programs.