Abstract
To the best of our knowledge, this paper presents the first application of Molecular Dynamics to the Protein Folding Problem using the 3D AB model of proteins. Protein folding pathways are also presented and discussed. This work also offered new reference values for five benchmark sequences. Future works will investigate parallel versions of the presented approach and more experiments to create new bechmarks.
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References
Anfinsen, C.B.: Principles that govern the folding of protein chains. Science 181(96), 223–230 (1973)
Bachmann, M., Arkm, H., Janke, W.: Multicanonical study of coarse-grained off-lattice models for folding heteropolymers. Physical Review E 71, 1–11 (2005)
Baker, D.: A suprising simplicity to protein folding. Nature 405, 39–42 (2000)
Benítez, C.M.V., Lopes, H.S.: Hierarchical parallel genetic algorithm applied to the three-dimensional HP side-chain protein folding problem. In: Proc. of the IEEE Int. Conf. on Systems, Man and Cybernetics, pp. 2669–2676 (2010)
Benítez, C.M.V., Scalabrin, M., Lopes, H.S., Lima, C.R.E.: Reconfigurable Hardware Computing for Accelerating Protein Folding Simulations Using the Harmony Search Algorithm and the 3D-HP-Side Chain Model. In: Xiang, Y., Cuzzocrea, A., Hobbs, M., Zhou, W. (eds.) ICA3PP 2011, Part II. LNCS, vol. 7017, pp. 363–374. Springer, Heidelberg (2011)
Berendsen, H.J.C., Postma, J.P.M., van Gusteren, W.F., DiNola, A., Haak, J.R.: Molecular dynamics with coupling to an external bath. Journal of Chemical Physics 81, 3684 (1984)
Crescenzi, P., Goldman, D., Papadimitrou, C., Piccolboni, A., Yannakakis, M.: On the complexity of protein folding. Journal of Computational Biolology 5, 423–446 (1998)
Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., et al.: Principles of protein folding - a perspective from simple exact models. Protein Science 4(4), 561–602 (1995)
Grosberg, A.Y., Khokhlov, A.R.: Statistical Physics of Macromolecules. AIP Press (1994)
Gruebele, M.: Protein folding: the free energy surface. Current Opinion in Structural Biology 12(1), 161–168 (2002)
Hunter, L.: Artificial Intelligence and Molecular Biology, 1st edn. AAAI Press, Boston (1993)
Irback, A., Peterson, C., Potthast, F., Sommelius, O.: Local interactions and protein folding: A three-dimensional off-lattice approach. Journal of Chemical Physics 1, 273–282 (1997)
Karplus, M.: The Levinthal paradox: yesterday and today. Folding & Design 2(4), S69–S75 (1997)
Kim, S.Y., Lee, S.B., Lee, J.: Structure optimization by conformational space annealing in an off-lattice protein model. Physical Review E 72, 1–6 (2005)
Liang, F.: Annealing contour monte carlo algorithm for structure optimization in an off-lattice protein model. Chemical Physics 120, 6756–6763 (2004)
Liwo, A., Khalili, M., Scheraga, H.A.: Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proceedings of the National Academy of Sciences 102(7), 2362–2367 (2005)
Mirny, L., Shakhnovich, E.: Protein foding theory: From lattice to all-atom models. Annual Review of Biophysics and Biomolecular Structure 30, 361–396 (2001)
Nishimura, C., Lietzow, M.A., Dyson, H.J., Wright, P.E.: Sequence determinants of a protein folding pathway. Journal of Molecular Biology 351, 383–392 (2005)
Day, R., Daggett, V.: All-atom simulations of protein folding and unfolding. Advances in Protein Chemistry 66, 373–403 (2003)
Rapaport, D.C.: The Art of Molecular Dynamics Simulation. Cambridge University Press (2004)
Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C.: Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics 23, 327–341 (1977)
Stillinger, F.H., Head-Gordon, T.: Collective aspects of protein folding illustrated by a toy model. Physical Review E 52(3), 2872–2877 (1995)
Swope, W.C., Andersen, H.C., Berens, P.H., Wilson, K.R.: A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters. The Journal of Chemical Physics 76, 637 (1982)
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Benítez, C.M.V., Lopes, H.S. (2012). Molecular Dynamics for Simulating the Protein Folding Process Using the 3D AB Off-Lattice Model. In: de Souto, M.C., Kann, M.G. (eds) Advances in Bioinformatics and Computational Biology. BSB 2012. Lecture Notes in Computer Science(), vol 7409. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31927-3_6
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DOI: https://doi.org/10.1007/978-3-642-31927-3_6
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