PROTEIN FOLDING, MOLECULAR DOCKING, DRUG DESIGN - The Role of the Derivative “Drift” in Complex Systems Dynamics

Corrado Giannantoni

Abstract

The relevance of Protein Folding is widely recognized. It is also well-known, however, that it is one of the dynamic problems in TDC considered as being intractable. In addition, even in the case of solutions obtainable in reasonable computation time, these always present a “drift” between the foreseen behavior of the biological system analyzed and the corresponding experimental results. A drift which is much more marked as the order of the system increases. Both the “intractability” of the problem and the above-mentioned “drifts”, as well as the insolubility of the problem in explicit terms (or at least in a closed form), can be overcome by starting from a different gnoseological approach. This suggests a new definition of derivative, the “incipient” derivative. The solution to the “Three-body Problem” obtained by means of IDC, and its extension to any number of bodies, allows us to assert that the folding of even a macroscopic protein, such as dystrophin for example, made up of about 100,000 atoms, can be carried out in a few minutes, when the model is run on next generation computers (1 Petaflop). The same methodology can also be applied to both Molecular Docking and computer-aided Drug Design.

References

  1. Brown M. T. and Herendeen R. A., 1996. Embodied Energy Analysis and Emergy analysis: a comparative view. Ecological Economics 19 (1996), 219-235.
  2. Giannantoni C., 1995. Linear Differential Equations with Variable Coefficients. Fundamental Theorem of the Solving Kernel. ENEA, Rome, RT/ERG/95/07.
  3. Giannantoni C., 2001a. The Problem of the Initial Conditions and Their Physical Meaning in Linear Differential Equations of Fractional Order. Applied Mathematics and Computation 141 (2003) 87-102.
  4. Giannantoni C., 2001b. Mathematical Formulation of the Maximum Em-Power Principle. Second Biennial International Emergy Conference. Gainesville (Florida, USA), September 20-22, 2001, pp. 15-33.
  5. Giannantoni C., 2002. The Maximum Em-Power Principle as the basis for Thermodynamics of Quality. Ed. S.G.E., Padua, ISBN 88-86281-76-5.
  6. Giannantoni C., 2004a. Differential Bases of Emergy Algebra. Third Emergy Evaluation and Research Conference. Gainesville (Florida, USA), January 29- 31, 2004.
  7. Giannantoni C., 2004b. Mathematics for Generative Processes: Living and Non-Living Systems. 11th International Congress on Computational and Applied Mathematics, Leuven, July 26-30, 2004. Applied Mathematics and Computation 189 (2006) 324-340.
  8. Giannantoni C., 2006. Emergy Analysis as the First Ordinal Theory of Complex Systems. Proceedings of the Fourth Emergy Conference 2006. Gainesville, Florida, USA, January 17-22, pp. 15.1-15.14.
  9. Giannantoni C., 2007a. Armonia delle Scienze (vol. I). La Leggerezza della Qualità. Ed. Sigraf, Pescara (Italy), ISBN 978-88-95566-00-9.
  10. Giannantoni C., 2007b. Ordinal Benefits vs Economic Benefits as a Reference Guide for Policy Decision Making. The Case of Hydrogen Technologies. Submitted to Energy (February 2008). In press.
  11. Giannantoni C., 2008a. From Transformity to Ordinality, or better: from Generative Transformity to Ordinal Generativity. Proceedings of the Fifth Emergy Conference. Gainesville, Florida, USA, January 31- February 2, 2008.
  12. Giannantoni C., 2008b. Armonia delle Scienze (vol. II). L'Ascendenza della Qualità. Edizioni Sigraf, Pescara (Italy), ISBN 978-88-95566-18-4.
  13. Landau L. and Lifchitz E., 1969. Mécanique. Ed. MIR, Moscow.
  14. Odum H. T., 1988. Self-Organization, Transformity and Information Science, v. 242, pp. 1132-1139, November 25.
  15. Odum H. T., 1994a. Ecological and General Systems. An Introduction to Systems Ecology. Re. Edition. University Press Colorado.
  16. Odum H. T., 1994b. Environmental Accounting. Environ. Engineering Sciences. University of Florida.
  17. Odum H. T., 1994c. Self Organization and Maximum Power. Environ. Engineering Sciences. University of Florida.
  18. Oldham K. B. and Spanier J., 1974. The Fractional Calculus. Theory and Applications of Differentiation and Integration to Arbitrary Order. Academic Press, Inc., London.
  19. Poincaré H., 1889. Les Méthodes Nouvelles de la Mécanique Céleste. Ed. Librerie Scientifique et Technique A. Blachard. Vol. I, II, III, Paris, 1987.
  20. Shivaani K. et al. 2009. Phase 0 Clinical Trial of the Poly (ADP-Ribose) Polymerase Inhibitor ABT-888 in Patients with Advanced Malignancies. Journal of Clinical Oncology. Published Ahead of Print on April 13, 2009 as 10.1200/JCO.2008.19.7681.
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Paper Citation


in Harvard Style

Giannantoni C. (2010). PROTEIN FOLDING, MOLECULAR DOCKING, DRUG DESIGN - The Role of the Derivative “Drift” in Complex Systems Dynamics . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 193-199. DOI: 10.5220/0002763401930199


in Bibtex Style

@conference{bioinformatics10,
author={Corrado Giannantoni},
title={PROTEIN FOLDING, MOLECULAR DOCKING, DRUG DESIGN - The Role of the Derivative “Drift” in Complex Systems Dynamics},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={193-199},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002763401930199},
isbn={978-989-674-019-1},
}


in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - PROTEIN FOLDING, MOLECULAR DOCKING, DRUG DESIGN - The Role of the Derivative “Drift” in Complex Systems Dynamics
SN - 978-989-674-019-1
AU - Giannantoni C.
PY - 2010
SP - 193
EP - 199
DO - 10.5220/0002763401930199