BACKGROUND: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. RESULTS: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. CONCLUSIONS: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.

In this paper, the analytic 3-RPR platform studied by Wenger and Chablat in 2009 will be analyzed regarding its cuspidality condition. Many investigations have paid great attention to the cuspidality phenomena that arise for some designs of the 3-RPR parallel manipulator. Nevertheless, most of them focus on obtaining the cusp points of direct kinematic singularity curves on a section of the joint space, meaning that one of the input variables must remain constant. The authors, in this paper, obtain the locus of cusp points of the manipulator under study in a complete analytic way and in 3-D joint space. This way, the three inputs can be actuated to perform a nonsingular transition that encircles one of the curves that belong to the locus of cusp points. It will be shown that the duplicity of one of the output variables of this manipulator causes the overlapping of two different cusp points in the joint space. In order to visualize this characteristic, initially, transitions in a section of the joint space will be analyzed using, additionally, the reduced configuration space. Then, transitions in the 3-D joint space will be performed, showing that, in order to ensure a feasible nonsingular transition, it is necessary to represent the direct kinematic singularity surface and assess the evolution of the three output variables along the trajectory.

It is known that there are parallel manipulators that can perform nonsingular transitions between different assembly modes. In particular, 3-degree-of-freedom (DOF) manipulators have received primary attention related to this phenomenon. In this paper, the conditions for the existence of special points in the projection of the direct-kinematic-problem-singularity locus onto the joint space for one constant input are obtained. From these conditions, the coordinates of all cusp points can be obtained analytically. Encircling one of these cusp points, it is possible to make a nonsingular transition between two assembly modes of a parallel manipulator. Utilizing these conditions, the range for the existence of cusp points of each input value can be also determined. An extension of the concept of cusp points to the complete joint space is also performed. The procedure is applied to an RPR-2-PRR parallel manipulator that can be solved analytically. Its dimensional variables are parametrized as a 1-D function, and all results are obtained in closed form, which is a benchmark example for other procedures.

This paper presents the application of the procedure known as the Geometrical-Iterative Method to the resolution of the direct position problem in spatial mechanisms, and in particular parallel platforms. This procedure is based on the successive application of geometric constraints used for modelling the mechanism. The application sequence of these is defined from a search algorithm directed at satisfying two basic convergence conditions. The method is a competitive alternative for the Newton-Raphson procedure in the kinematic control of parallel platforms.