VM2: Flexible ligand and protein

Molecular Flexibility as Required

Ligand molecules

All atoms in ligands and other small molecules (600 atoms or less) are always free to move unless the user chooses to apply  constraints, such as harmonic or flat bottomed well potentials on particular atoms or groups of atoms. Such constraints can be useful for pre-generation of ligand R-group conformations, while maintaining a lead molecule’s scaffold conformation.

Protein molecules

All protein atoms can, in principle, be flexible in VM2 calculations. However, in practice, this is not required to achieve good binding affinity predictions, and it is computationally more efficient to partition the protein system into mobile, fixed, and excluded sets of atoms.