A weighted HP model for protein folding with diagonal contacts

Hans-Joachim Böckenhauer; Dirk Bongartz

RAIRO - Theoretical Informatics and Applications (2007)

  • Volume: 41, Issue: 4, page 375-402
  • ISSN: 0988-3754

Abstract

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The HP model is one of the most popular discretized models for attacking the protein folding problem, i.e., for the computational prediction of the tertiary structure of a protein from its amino acid sequence. It is based on the assumption that interactions between hydrophobic amino acids are the main force in the folding process. Therefore, it distinguishes between polar and hydrophobic amino acids only and tries to embed the amino acid sequence into a two- or three-dimensional grid lattice such as to maximize the number of contacts, i.e., of pairs of hydrophobic amino acids that are embedded into neighboring positions of the grid. In this paper, we propose a new generalization of the HP model which overcomes one of the major drawbacks of the original HP model, namely the bipartiteness of the underlying grid structure which severely restricts the set of possible contacts. Moreover, we introduce the (biologically well-motivated) concept of weighted contacts, where each contact gets assigned a weight depending on the spatial distance between the embedded amino acids. We analyze the applicability of existing approximation algorithms for the original HP model to our new setting and design a new approximation algorithm for this generalized model.

How to cite

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Böckenhauer, Hans-Joachim, and Bongartz, Dirk. "A weighted HP model for protein folding with diagonal contacts." RAIRO - Theoretical Informatics and Applications 41.4 (2007): 375-402. <http://eudml.org/doc/249931>.

@article{Böckenhauer2007,
abstract = { The HP model is one of the most popular discretized models for attacking the protein folding problem, i.e., for the computational prediction of the tertiary structure of a protein from its amino acid sequence. It is based on the assumption that interactions between hydrophobic amino acids are the main force in the folding process. Therefore, it distinguishes between polar and hydrophobic amino acids only and tries to embed the amino acid sequence into a two- or three-dimensional grid lattice such as to maximize the number of contacts, i.e., of pairs of hydrophobic amino acids that are embedded into neighboring positions of the grid. In this paper, we propose a new generalization of the HP model which overcomes one of the major drawbacks of the original HP model, namely the bipartiteness of the underlying grid structure which severely restricts the set of possible contacts. Moreover, we introduce the (biologically well-motivated) concept of weighted contacts, where each contact gets assigned a weight depending on the spatial distance between the embedded amino acids. We analyze the applicability of existing approximation algorithms for the original HP model to our new setting and design a new approximation algorithm for this generalized model. },
author = {Böckenhauer, Hans-Joachim, Bongartz, Dirk},
journal = {RAIRO - Theoretical Informatics and Applications},
keywords = {Protein folding; HP model; approximation algorithms},
language = {eng},
month = {8},
number = {4},
pages = {375-402},
publisher = {EDP Sciences},
title = {A weighted HP model for protein folding with diagonal contacts},
url = {http://eudml.org/doc/249931},
volume = {41},
year = {2007},
}

TY - JOUR
AU - Böckenhauer, Hans-Joachim
AU - Bongartz, Dirk
TI - A weighted HP model for protein folding with diagonal contacts
JO - RAIRO - Theoretical Informatics and Applications
DA - 2007/8//
PB - EDP Sciences
VL - 41
IS - 4
SP - 375
EP - 402
AB - The HP model is one of the most popular discretized models for attacking the protein folding problem, i.e., for the computational prediction of the tertiary structure of a protein from its amino acid sequence. It is based on the assumption that interactions between hydrophobic amino acids are the main force in the folding process. Therefore, it distinguishes between polar and hydrophobic amino acids only and tries to embed the amino acid sequence into a two- or three-dimensional grid lattice such as to maximize the number of contacts, i.e., of pairs of hydrophobic amino acids that are embedded into neighboring positions of the grid. In this paper, we propose a new generalization of the HP model which overcomes one of the major drawbacks of the original HP model, namely the bipartiteness of the underlying grid structure which severely restricts the set of possible contacts. Moreover, we introduce the (biologically well-motivated) concept of weighted contacts, where each contact gets assigned a weight depending on the spatial distance between the embedded amino acids. We analyze the applicability of existing approximation algorithms for the original HP model to our new setting and design a new approximation algorithm for this generalized model.
LA - eng
KW - Protein folding; HP model; approximation algorithms
UR - http://eudml.org/doc/249931
ER -

References

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  7. K.A. Dill, Theory for the folding and stability of globular proteins. Biochemistry24 (1985) 1501.  
  8. K.A. Dill, S. Bromberg, K. Yue, K. Fiebig, D. Yee, P. Thomas and H. Chan, Principles of protein folding – a perspective from simple exact models. Protein Sci.4 (1995) 561–602.  
  9. W.E. Hart and S. Istrail, Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal. J. Comput. Biol.3 (1996) 53–96.  
  10. A. Newman, A New Algorithm for Protein Folding in the HP Model, in Proc. of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'02) (2002) 876–884.  

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