A weighted HP model for protein folding with diagonal contacts
RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications, Tome 41 (2007) no. 4, pp. 375-402.

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.

DOI : https://doi.org/10.1051/ita:2007023
Classification : 68W25,  92C40
Mots clés : protein folding, HP model, approximation algorithms
     author = {B\"ockenhauer, Hans-Joachim and Bongartz, Dirk},
     title = {A weighted {HP} model for protein folding with diagonal contacts},
     journal = {RAIRO - Theoretical Informatics and Applications - Informatique Th\'eorique et Applications},
     pages = {375--402},
     publisher = {EDP-Sciences},
     volume = {41},
     number = {4},
     year = {2007},
     doi = {10.1051/ita:2007023},
     mrnumber = {2377969},
     language = {en},
     url = {http://www.numdam.org/articles/10.1051/ita:2007023/}
AU  - Böckenhauer, Hans-Joachim
AU  - Bongartz, Dirk
TI  - A weighted HP model for protein folding with diagonal contacts
JO  - RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications
PY  - 2007
DA  - 2007///
SP  - 375
EP  - 402
VL  - 41
IS  - 4
PB  - EDP-Sciences
UR  - http://www.numdam.org/articles/10.1051/ita:2007023/
UR  - https://www.ams.org/mathscinet-getitem?mr=2377969
UR  - https://doi.org/10.1051/ita:2007023
DO  - 10.1051/ita:2007023
LA  - en
ID  - ITA_2007__41_4_375_0
ER  - 
Böckenhauer, Hans-Joachim; Bongartz, Dirk. A weighted HP model for protein folding with diagonal contacts. RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications, Tome 41 (2007) no. 4, pp. 375-402. doi : 10.1051/ita:2007023. http://www.numdam.org/articles/10.1051/ita:2007023/

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