The Molecular Distance Geometry Problem (MDGP) is the problem
of finding the possible conformations of a molecule by exploiting available information
about distances between some atom pairs. When particular assumptions
are satisfied, the MDGP can be discretized, so that the search domain of the
problem becomes a tree. This tree can be explored by using an interval Branch & Prune
(*i*BP) algorithm. In this context, the order given to the atoms of the
molecules plays an important role. In fact, the discretization assumptions are
strongly dependent on the atomic ordering, which can also impact the computational
cost of the *i*BP algorithm. In this work, we propose a new partial discretization
order for protein backbones. This new atomic order optimizes a set of
objectives, that aim at improving the *i*BP performances. The optimization of the
objectives is performed by Answer Set Programming (ASP), a declarative programming
language that allows to express our problem by a set of logical constraints.
The comparison with previously proposed orders for protein backbones
shows that this new discretization order makes *i*BP perform more efficiently.