AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening) employs an automatic procedure for energy minimization of protein-ligands complexes (package AMMOS_ProtLig) or of small chemical compounds present in a library (package AMMOS_SmallMol). As such, the software offers valuable solutions to assist structure-based in silico screening experiments or ligand-based projects. The package makes use of molecular mechanics concepts and is based on the program AMMP [2-3], available under GNU license (http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html). AMMOS has been developed in the INSERM – University Paris Diderot, lab. Bioinformatics-MTI (http://www.vls3d.com/). The package AMMOS is written in C and Python and is available for Linux and Mac OS X systems under the GNU General Public license.