dock

The new features of DOCK 6 include: genetic algorithms and de novo design for fragment based ligand searching; additional scoring options during minimization; DOCK 3.5 scoring-including Delphi electrostatics, ligand conformational entropy corrections, ligand desolvation, receptor desolvation; Hawkins-Cramer-Truhlar GB/SA solvation scoring with optional salt screening; and AMBER scoring-including receptor flexibility, the full AMBER molecular mechanics scoring function with implicit solvent, conjugate gradient minimization, and molecular dynamics simulation capabilities. Because DOCK 6 is an extension of DOCK 5, it also includes all previous features. (Summary from the program web page.)

The official web page: https://dock.compbio.ucsf.edu/DOCK_6/index.htm