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Almost FPRAS for Lattice Models of Protein Folding

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Experimental and Efficient Algorithms (WEA 2005)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 3503))

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Abstract

The provably efficient randomized approximation scheme which evaluates the partition function for the wide class of lattice models of protein prediction is presented. We propose to apply the idea of self-testing algorithms introduced recently in [8]. We consider the protein folding process which is simplified to a self-avoiding walk on a lattice. The power of a simplified approach is in its ability to search the conformation space, to train the search parameters and to test basic assumptions about the nature of the protein folding process. Our main theoretical results are formulated in the general setting, i.e. we do not assume any specific lattice model. For the simulation study we have chosen the HP model on the FCC lattice.

Research supported by Polish Research Council KBN grant 4 T11C 044 25.

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© 2005 Springer-Verlag Berlin Heidelberg

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Gambin, A., Wójtowicz, D. (2005). Almost FPRAS for Lattice Models of Protein Folding. In: Nikoletseas, S.E. (eds) Experimental and Efficient Algorithms. WEA 2005. Lecture Notes in Computer Science, vol 3503. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11427186_46

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  • DOI: https://doi.org/10.1007/11427186_46

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25920-6

  • Online ISBN: 978-3-540-32078-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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