title: Insights into mechanism kinematics for protein motion simulation.
abstract: 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.
authors.affiliation: Faculty of Engineering in Bilbao, University of the Basque Country UPV/EHU, Department of Mechanical Engineering, Alameda de Urquijo s/n, 48013 Bilbao, Spain. mikel.diez@ehu.es.
authors.forename: Mikel
authors.initials: M
authors.lastname: Diez
authors.forename: Víctor
authors.initials: V
authors.lastname: Petuya
authors.forename: Luis Alfonso
authors.initials: LA
authors.lastname: Martínez-Cruz
authors.forename: Alfonso
authors.initials: A
authors.lastname: Hernández
mesh_terms: D000465:Algorithms; D007700:Kinetics; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000032:analysis* / Q000737:chemistry
chemical_list: D011506:Proteins