Molecular Structure for Optimization in situ with MMFF94
SZYBKI  optimizes molecular structures with the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures for use as input to other programs. Since the chemistry of molecular interactions is a matter of shape and electrostatics, it is impossible to consider either without reasonable 3D molecular structures.
SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.
Freeform is a new utility program included with SZYBKI that provides two functionalities (1) the solvation energy of the free ligand, (2) the free energy of going from an ensemble of solution phase conformers to a single, bioactive conformation.
For more detailed information on SZYBKI, check out the links below:
Documentation > Evaluate