ALBERT

Description: Background: The high demanding computational requirements necessary to carry out protein motion simulationsmake it difficult to obtain information related to protein motion. On the one hand, moleculardynamics simulation requires huge computational resources to achieve satisfactory motionsimulations. On the other hand, less accurate procedures such as interpolation methods, do notgenerate realistic morphs from the kinematic point of view. Analyzing a protein¿s movement is verysimilar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composedof rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen,based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmapmethod, which discretizes the protein configurational space against a scoring function, or thekinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulateprotein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics ispresented. The paper describes a set of methodologies, combining different techniques such asstructure normalization normalization processes, simulation algorithms and secondary structuredetection procedures. The combination of all these procedures allows to obtain kinematic morphs ofproteins achieving a very good computational cost-error rate, while maintaining the biologicalmeaning 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 theconformational change suffered by a protein when exerting its function. The combination of a mainsimulation procedure assisted by a secondary structure process, and a side chain orientation strategy,allows to obtain a fast and reliable simulations of protein motion.