3D protein structure prediction.

Amber (Assisted Model Building with Energy Refinement) "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

AutoDock Vina is an open-source program for doing molecular docking.

DOCK (also called UCSF Dock) is molecular modeling program used to identify potential binding geometries and interactions of a molecule to a target.

GROMACS is a versatile package to perform molecular dynamics, i.e.simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

HOOMD-blue is a general-purpose particle simulation toolkit optimized for execution on both GPUs and CPUs.

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

MOBCAL is a program to calculate mobilities.