Advertisement

Reconfigurable Hardware Computing for Accelerating Protein Folding Simulations Using the Harmony Search Algorithm and the 3D-HP-Side Chain Model

  • César Manuel Vargas Benítez
  • Marlon Scalabrin
  • Heitor Silvério Lopes
  • Carlos R. Erig Lima
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7017)

Abstract

Proteins are essentials to life and they have countless biological functions. They are synthesized in the ribosome of cells following a template given by the messenger RNA (mRNA). During the synthesis, the protein folds into an unique three-dimensional structure, known as native conformation. This process is called protein folding. Several diseases are believed to be result of the accumulation of ill-formed proteins.Therefore, understanding the folding process can lead to important medical advancements and development of new drugs.

Keywords

Harmony Search Harmony Search Algorithm Harmony Memory Pitch Adjust Rate Functional Block Diagram 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Anfinsen, C.B.: Principles that govern the folding of protein chains. Science 181(96), 223–230 (1973)CrossRefGoogle Scholar
  2. 2.
    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)Google Scholar
  3. 3.
    Berger, B., Leighton, F.T.: Protein folding in the hydrophobic-hydrophilic HP model is NP-complete. Journal of Computational Biology 5(1), 27–40 (1998)CrossRefGoogle Scholar
  4. 4.
    Dandass, Y.S., Burgess, S.C., Lawrence, M., Bridges, S.M.: Accelerating string set matching in FPGA hardware for bioinformatics research. BMC Bioinformatics 9(197) (2008)Google Scholar
  5. 5.
    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)CrossRefGoogle Scholar
  6. 6.
    Geem, Z.W., Kim, J.-H., Loganathan, G.V.: A new heuristic optimization algorithm: Harmony search. Simulation 76(2), 60–68 (2001)CrossRefGoogle Scholar
  7. 7.
    Armstrong Junior, N.B., Lopes, H.S., Lima, C.R.E.: Preliminary steps towards protein folding prediction using reconfigurable computing. In: Proc. 3rd Int. Conf. on Reconfigurable Computing and FPGAs, pp. 92–98 (2006)Google Scholar
  8. 8.
    Li, M.S., Klimov, D.K., Thirumalai, D.: Folding in lattice models with side chains. Computer Physics Communications 147(1), 625–628 (2002)CrossRefzbMATHGoogle Scholar
  9. 9.
    Lopes, H.S.: Evolutionary algorithms for the protein folding problem: A review and current trends. In: Smolinski, T.G., Milanova, M.G., Hassanien, A.-E. (eds.) Computational Intelligence in Biomedicine and Bioinformatics. SCI, vol. 151, pp. 297–315. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  10. 10.
    Maruo, M.H., Lopes, H.S., Delgado, M.R.B.: Self-adapting evolutionary parameters: Encoding aspects for combinatorial optimization problems. In: Raidl, G.R., Gottlieb, J. (eds.) EvoCOP 2005. LNCS, vol. 3448, pp. 154–165. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  11. 11.
    Ramdas, T., Egan, G.: A survey of FPGAs for acceleration of high performance computing and their application to computational molecular biology. In: Proc. of the IEEE TENCON, pp. 1–6 (2005)Google Scholar
  12. 12.
    Sung, W.-T.: Efficiency enhancement of protein folding for complete molecular simulation via hardware computing. In: Proc. 9th IEEE Int. Conf. on Bioinformatics and Bioengineering, pp. 307–312 (2009)Google Scholar
  13. 13.
    Xia, F., Dou, Y., Lei, G., Tan, Y.: FPGA accelerator for protein secondary structure prediction based on the GOR algorithm. BMC Bioinformatics 12, S5 (2011)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • César Manuel Vargas Benítez
    • 1
  • Marlon Scalabrin
    • 1
  • Heitor Silvério Lopes
    • 1
  • Carlos R. Erig Lima
    • 1
  1. 1.Bioinformatics LaboratoryFederal University of Technology - ParanáCuritibaBrazil

Personalised recommendations