Geometry engines are used to build, manipulate, and measure three-dimensional molecular structures. Structures can be built from standard bond angle and length data or using distance geometry-based methods. When coupled to a computational engine, geometry engines (e.g. minimization, sampling, dynamics, Monte Carlo, and perturbation) can be used to evaluate structural variation as a function of energy and to perform statistical mechanics analyses. Different combinations of computational and geometry engines can be used to study such problems as conformational energy surfaces and transitions, reaction pathways, and intermolecular interactions (i.e. complexes). Other geometry engines can be used to fit molecular structures for the purpose of comparison.