Examining Protein Folding Process Simulation and Searching for Common Structure Motifs in a Protein Family as Experiments in the GridSpace2 Virtual Laboratory

  • Tomasz Jadczyk
  • Maciej Malawski
  • Marian Bubak
  • Irena Roterman
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7136)


This paper presents two in-silico experiments from the field of bioinformatics. The first experiment covers the popular problem of protein folding process simulation and investigates the correctness of the “Fuzzy Oil Drop” model (FOD) [3], on over 60 thousands of proteins deposited in Protein Data Bank [18]. The FOD model assumes the hydrophobicity distribution in proteins to be accordant with the 3D Gauss function differentiating the hydrophobicity density from the highest in the center of the molecule, to zero level on the surface. The second experiment focuses on performing comparison of proteins that belong to the same family. Examination of proteins alignment at three different levels of protein description may lead to identifying a conservative area in protein family, which is responsible for the protein function. It also creates a possibility of determining a ligand binding site for protein, which is a key issue in drug design. Both experiments were realized as virtual experiments in the GridSpace2 Virtual Laboratory [13] Experiment Workbench [16] and were executed on Zeus cluster provided by PL-Grid.


virtual laboratory in-silico experiment bioinformatics protein folding fuzzy oil drop model protein function protein comparison 


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  1. 1.
    Baxevanis, A.D., Ouellette, F.B.F.; Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Wiley-Interscience (2001) ISBN (0471383910)Google Scholar
  2. 2.
    Higgs, P.G., Attwood, T.: Bioinformatics and Molecular Evolution. Blackwell Publishing Limited (2005) ISBN (1405106832)Google Scholar
  3. 3.
    Konieczny, L., Brylinski, M., Roterman, I.: Gauss-function-based model of hydrophobicity density in proteins. Silico. Biol. 6, 15–22 (2006)Google Scholar
  4. 4.
    Brylinski, M., Konieczny, L., Kononowicz, A., Roterman, I.: Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family. Journal of Theoretical Biology 251, 275–285 (2008)MathSciNetCrossRefGoogle Scholar
  5. 5.
    Brylinski, M., Konieczny, L., Roterman, I.: SPI – structure predictability index for protein sequences. Silico. Biol. 5, 22 (2004)Google Scholar
  6. 6.
    Jurkowski, W., Brylinski, M., Konieczny, L., Wisniowski, Z., Roterman, I.: Conformational subspace in simulation of early-stage protein folding. Proteins 55(91), 115–127 (2004)CrossRefGoogle Scholar
  7. 7.
    Roterman, I.: The geometrical analysis of peptide backbone structure and its local deformations. Biochimie. 77(3), 204–216 (1995)CrossRefGoogle Scholar
  8. 8.
    Roterman, I.: Modelling the optimal simulation path in the peptide chain folding – studies based on geometry of alanine heptapeptide. J. Theor. Biol. 177(3), 283–288 (1995)CrossRefGoogle Scholar
  9. 9.
    Kauzmann, W.: Adv. Protein Chem. 14, 1 (1959)Google Scholar
  10. 10.
    Levitt, M.: A Simplified Representation of Protein Conformations for Rapid Simulation of Protein Folding. J. Mol. Biol. 104, 59–107 (1976)CrossRefGoogle Scholar
  11. 11.
    Nalewajski, R.F.: Information theory of molecular systems. Elsevier (2006) ISBN 978-0-444-51966-5 Google Scholar
  12. 12.
    Chou, K.C.: Review: structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry 11, 2105–2134 (2004)CrossRefGoogle Scholar
  13. 13.
    Ciepiela, E., Harężlak, D., Kocot, J., Bartyński, T., Kasztelnik, M., Nowakowski, P., Gubała, T., Malawski, M., Bubak, M.: Exploratory Programming in the Virtual Laboratory. In: Proceedings of the International Multiconference on Computer Science and Information Technology, pp. 621–628 (2010)Google Scholar
  14. 14.
    Ciepiela, E., Nowakowski, P., Kocot, J., Harężlak, D., Gubała, T., Meizner, J., Kasztelnik, M., Bartyński, T., Malawski, M., Bubak, M.: Managing Entire Lifecycles of e-Science Applications in the GridSpace2 Virtual Laboratory – from Motivation through Idea to Operable Web-Accessible Environment Built on Top of PL-Grid e-Infrastructure. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 228–239. Springer, Heidelberg (2012)Google Scholar
  15. 15.
    Ciepiela, E., Zaraska, L., Sulka, G.D.: GridSpace2 Virtual Laboratory Case Study: Implementation of Algorithms of Quantitative Analysis of the Grain Morphology in Self-Assembled Hexagonal Lattices according to Hillebrand Method. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 240–251. Springer, Heidelberg (2012)Google Scholar
  16. 16.
    GridSpace2 Experiment Workbench – portal for PL-Grid users,
  17. 17.
    Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M., Li, P., Oinn, T.: Taverna: a tool for building and running workflows of services. Nucleic Acids Research 34(Web Server issue), 729–732 (2006)CrossRefGoogle Scholar
  18. 18.
    Research Collaboratory for Structural Bioinformatics, Protein Data Bank,
  19. 19.
    Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., Mcgettigan, P.A., Mcwilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., Higgins, D.G.: Clustal W and Clustal X version 2.0. Bioinformatics 23(21) (2007)Google Scholar
  20. 20.
    Ortiz, A.R., Strauss, C.E., Olmea, O.: MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Science: A Publication of the Protein Society 11, 2606–2621 (2002)CrossRefGoogle Scholar
  21. 21.
    Ruby programming language,
  22. 22.
    Python programming language,
  23. 23.
    Biopython – a set of freely available tools for biological computation,

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Tomasz Jadczyk
    • 1
  • Maciej Malawski
    • 2
  • Marian Bubak
    • 2
    • 3
  • Irena Roterman
    • 4
  1. 1.ACC Cyfronet AGHAGH University of Science and TechnologyKrakówPoland
  2. 2.Department of Computer ScienceAGH University of Science and TechnologyKrakówPoland
  3. 3.Informatics InstituteUniversity of AmsterdamThe Netherlands
  4. 4.Medical College, Department of Bioinformatics and TelemedicineJagiellonian UniversityKrakówPoland

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