-relax:respect_resfileoption, the relax application can be used for design.
Match: Place a small molecule into a protein pocket so it satisfies given geometric constraints.
OOP design: Design proteins with oligooxopiperazine residues.
DougsDockDesignMinimize: Redesign the protein/peptide interface of Calpain and a fragment of its inhibitory peptide calpastatin.
theta ligand: Calculate the fraction of ligand that is exposed to the solvent in a protein-ligand complex.