Antonio Mucherino – Optimization Online

The iBP algorithm for the discretizable molecular distance geometry problem with interval data

Published: 2011/01/20

Biomedical Applications, Combinatorial Optimization combinatorial reformulation, distance geometry, interval branch and prune, nmr data, protein molecules

The Distance Geometry Problem in three dimensions consists in finding an embedding in R^3 of a given nonnegatively weighted simple undirected graph such that edge weights are equal to the corresponding Euclidean distances in the embedding. This is a continuous search problem that can be discretized under some assumptions on the minimum degree of the … Read more

Molecular distance geometry methods: from continuous to discrete

Published: 2009/09/27, Updated: 2009/10/03

Biomedical Applications, Combinatorial Optimization branch-and-prune, distance geometry, network localization, rigidity

Distance geometry problems arise from the need to position entities in the Euclidean $K$-space given some of their respective distances. Entities may be atoms (molecular distance geometry), wireless sensors (sensor network localization), or abstract vertices of a graph(graph drawing). In the context of molecular distance geometry, the distances are usually known because of chemical properties … Read more