Abstract
In this article a methodology for simulating proteins function movement is presented. The procedure uses a potential energy feedback algorithm that without minizing the energy obtains succesive positions of the protein. before the simulation process, structures are normalized reducing the experimental methods produced errors. The procedure presents a low computational cost in relation to the accuracy obtained. Finally, results of the simulation for a specific protein are shown.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Chirikjian, G.S., A methodology for determining mechanical properties of macromolecules from ensemble motion data. Trends in Analytical Chemistry 22:549–553, 2003.
Cornell, W.D., Cieplak, P., Byly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., and Kollman, P.A., A second generation force field for the simulations of proteins nucleic acids and organic molecules. Journal of American Chemical Society 117:5179–5197, 1995.
Diez, M., Petuya, V., Urizar, M., and Hernandez, A., A biokinematic computational procedure for protein function simulation. In IEEE Conference Proceedings pp. 355–362, 2009.
Kavraki, L.E., Protein-ligand docking, including flexible receptor-flexible ligand docking. Technical Report, Creative Commons, 2007.
Kazerounian, K., Laif, K., and Alvarado, C., Protofold: A successive kinetostatic compliance method for protein conformation prediction. Journal of Mechanism Design, 127:712–717, 2005.
Kazerounian, K. and Subramanian, R., Residue level inverse kinematics of peptide chains in presence of observation inaccurancies and bond lenght changes. Journal of Mechanism Design, 129:312–319, 2007.
Pauling, L. and Corey, R.B., Atomic coordinates and structure factors for two helical configurations of polypeptide chains. Proceedings of the National Academi of Sciences, 37, 1951.
Ramachandran, G.N., Ramakrishnan, C., and Sasisekharan, V., Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7:95–99, 1963.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media B.V.
About this paper
Cite this paper
Diez, M., Petuya, V., Macho, E., Hermández, A. (2010). Protein Kinematic Motion Simulation Including Potential Energy Feedback. In: Pisla, D., Ceccarelli, M., Husty, M., Corves, B. (eds) New Trends in Mechanism Science. Mechanisms and Machine Science, vol 5. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9689-0_10
Download citation
DOI: https://doi.org/10.1007/978-90-481-9689-0_10
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-90-481-9688-3
Online ISBN: 978-90-481-9689-0
eBook Packages: EngineeringEngineering (R0)