Assigned and unassigned distance geometry: applications to biological molecules and nanostructures (Q503659)

The present survey paper focuses on the applications of distance geometry to the studies of biological molecules and nanostructures. Distance geometry is the study of geometry and structure based on the notion of distance. In most applications, an incomplete list of distances between pairs of points (vertices) is given and the goal is to find positions for these vertices in some Euclidean space realizing the given distances. Moreover, sometimes the distances are not pre-assigned to specific pairs of objects and therefore, this information is a part of the solution. The first described problem is known as \textit{assigned distance geometry problem} and the second one is the \textit{unassigned distance geometry problem}. In the beginning of the paper, the definition and some historical information relating the problem is explained. In Section 2, the uniqueness of the distance geometry problem is discussed. Since the goal is to find a realization of vertices in the Euclidean space such that they are consistent with a given list \(\mathcal{D}\) of distances, the natural question is the following: given a list \(\mathcal{D}\) of distances, is there more than one realization? In some practical applications, the information about the pairs of vertices that corresponds to a given known distance is not provided. Therefore, in Section 3, some recent methods and algorithms for the unassigned distance geometry problem are described. In the following section, the discretization of the assigned distance geometry problem is considered. This is useful in some cases where the number of given distances is too small to guarantee rigidity. In Section 5, some applications of the distance geometry problem are given. The first main application is identification of three-dimensional conformations of biological molecules. In this area, some new approaches to distance measurements in biological and inorganic materials have been developed recently. The second main application is the problem of finding the atomic positions in some nanostructures. Moreover, an example is added showing that it is possible to reconstruct the \(C_{60}\) fullerene from unassigned distance lists extracted from real experiments.