Methods to predict the structure of a protein often rely on the knowledge of macro-sub-structures and their exact or approximate 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, thus, a critical problem in predicting protein conformations that are biologically realistic. This paper introduces a constraint that models a general multi-body system, and shows its application to the protein loop modeling, based on fragments assembly, along with filtering techniques, inspired by inverse kinematics, that can drastically reduce the search space of potential conformations.