# 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

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topBöckenhauer, 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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- H.-J. Böckenhauer and D. Bongartz, Protein folding in the HP model on grid lattices with diagonals. Discrete Appl. Math.155 (2007) 230–256. Extended Abstract in Proc. of the 29th International Symposium on Mathematical Foundations of Computer Science (MFCS'04). Lect. Notes Comput. Sci.3153 (2004) 227–238. Zbl1104.92021
- V. Chandra, A. DattaSharma and V.S.A. Kumar, The algorithmics of folding proteins on lattices. Discrete Appl. Math.127 (2003) 145–161. Zbl1038.92013
- P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni and M. Yannakakis, On the complexity of protein folding. J. Comput. Biol.5 (1998) 423-466. Extended Abstract in Proc. of the 30th Annual ACM Symposium on the Theory of Computing (STOC 1998) (1998) 597–603. Zbl1007.68511
- K.A. Dill, Theory for the folding and stability of globular proteins. Biochemistry24 (1985) 1501.
- 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.
- 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. Zbl0978.68528
- 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. Zbl1052.92026

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