Summary
The detailed study of folding and unfolding events in proteins is becoming central to develop rational therapeutic strategies against maladies such as Alzheimer and Parkinson disease. A promising approach to study the unfolding processes of proteins is through computer simulations. However, these computer simulations generate huge amounts of data that require computational methods for their analysis.
In this paper we report on the use of Inductive Logic Programming (ILP) techniques to analyse the trajectories of protein unfolding simulations. The paper describes ongoing work on one of several problems of interest in the protein unfolding setting. The problem we address here is that of explaining what makes secondary structure elements to break down during the unfolding process. We tackle such problem collecting examples of contexts where secondary structures break and (automatically) constructing rules that may be used to suggest the explanations.
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References
Brito, R.M.M., Dubitzky, W., Rodrigues, J.R.: Protein folding and unfolding simulations: A new challenge for data mining. OMICS: A Journal of Integrative Biology 8, 153–166 (2004)
Dzeroski, S.: Relational Data Mining. Springer, New York (2001)
Muggleton, S., De Raedt, L.: Inductive logic programming: Theory and methods. Journal of Logic Programming 19/20, 629–679 (1994)
Pande, V.S., Baker, I., Chapman, J., et al.: Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers 68, 91–109 (2003)
Shea, J.E., Brooks, C.L.: From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52, 499–535 (2001)
Srinivasan, A.: The Aleph Manual (2003), http://web.comlab.ox.ac.uk/oucl/research/areas/machlearn/Aleph
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Camacho, R., Alves, A., Silva, C.G., Brito, R.M.M. (2009). On Mining Protein Unfolding Simulation Data with Inductive Logic Programming. In: Corchado, J.M., De Paz, J.F., Rocha, M.P., Fernández Riverola, F. (eds) 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008). Advances in Soft Computing, vol 49. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85861-4_21
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DOI: https://doi.org/10.1007/978-3-540-85861-4_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-85860-7
Online ISBN: 978-3-540-85861-4
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