Methods to predict the structure of a protein often rely on the knowledge of macro sub-structures and their exact or approximated relative positions in space. The parts connecting these sub-structures are called loops and, in general, they are characterized by a high degree of freedom. The modeling of loops is a critical problem in predicting protein conformations that are biologically realistic. This paper introduces a class of constraints that models a general multi-body system; we present a proof of NP-completeness and provide filtering techniques, inspired by inverse kinematics, that can drastically reduce the search space of potential conformations. The paper shows the application of the constraint in solving the protein loop modeling problem, based on fragments assembly. © 2012 Springer-Verlag.