Abstract: Systems and methods for molecular structure generation and conformer elaboration, in which natural physical molecular movements can be combined with a molecular force field that constrains those movements, to rapidly produce conformational variants with relatively low energy. Construction and energy minimization of initial and subsequent 3D molecular models using force field parameters, are combined with alteration of the molecular model using biophysical transformations, to generate one or more conformations thereof. The biophysical transformations each include natural physical movements of parts of the molecule, such as rotation of atoms or bonds about a selected axis in the 3D molecular model. The selected axis can define ring components, selected bonds within a macrocyclic ring, selected bonds joining substituents or other portions of the molecule, or axes or lines defining one or more geometric features of the molecular model.