Protein Folding in the HP Model on Grid Lattices with Diagonals

  • Hans-Joachim Böckenhauer
  • Dirk Bongartz
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3153)


The protein folding problem, i.e., the computational prediction of the three-dimensional structure of a protein from its amino acid sequence, is one of the most important and challenging problems in computational biology. Since a complete simulation of the folding process of a protein is far too complex to handle, one tries to find an approximate solution by using a simplified, abstract model. One of the most popular models is the so-called HP model, where the hydrophobic interactions between the amino acids are considered to be the main force in the folding process, and furthermore the folding space is modelled by a two- or three-dimensional grid lattice.

In this paper, we will present some approximation algorithms for the protein folding problem in the HP model on an extended grid lattice with plane diagonals. The choice of this kind of lattice removes one of the major drawbacks of the original HP model, namely the bipartiteness of the grid which severely restricts the set of possible foldings. Our algorithms achieve an approximation ratio of \(\frac{26}{15}\approx 1.733\) for the two-dimensional and of \(\frac{8}{5}=1.6\) for the three-dimensional lattice. This improves significantly over the best previously known approximation ratios for the protein folding problem in the HP model on any lattice.


Approximation Algorithm Approximation Ratio Hydrophobic Amino Acid Input String Contact Edge 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Hans-Joachim Böckenhauer
    • 1
  • Dirk Bongartz
    • 1
  1. 1.Lehrstuhl für Informatik IRWTH AachenAachenGermany

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