Abstract: The present invention relates to a system and a method for constructing and associating a moduli space to a molecule or a model of a molecule. This mathematical representation of molecular structures enables the prediction of actual physical molecular structures. Molecular structures can be structures of macromolecules such as protein molecules and protein globules.

Abstract: Modelling a molecule by means of a graph, said graph comprising vertices and edges, each edge having a specific type, and said graph having cyclic orderings on the half-edges about at least one of the vertices, said system comprising means for determining the cyclic orderings on the half-edges about said at least one vertex by means of the spatial coordinates of the constituent atoms of the molecule, and means for determining the type of each edge of the graph by means of the relative spatial location of the constituent atoms of the molecule. Thereby automatic classification, comparison, specification, analysis and/or prediction of molecular structures can be provided because these molecular structures are represented by explicit combinatorial objects, and descriptors can be derived from the graph constructed in this manner. The descriptors are automatically computable from molecular databases, such as PDB or CATH, with no qualitative human intervention or subjective criteria.