Limits...
Protein folding in HP model on hexagonal lattices with diagonals.

Shaw D, Shohidull Islam AS, Sohel Rahman M, Hasan M - BMC Bioinformatics (2014)

Bottom Line: Since, this is a hard problem, a number of simplified models have been proposed in literature to capture the essential properties of this problem.In this paper we introduce the hexagonal lattices with diagonals to handle the protein folding problem considering the well researched HP model.We give two approximation algorithms for protein folding on this lattice.

View Article: PubMed Central - HTML - PubMed

ABSTRACT
Three dimensional structure prediction of a protein from its amino acid sequence, known as protein folding, is one of the most studied computational problem in bioinformatics and computational biology. Since, this is a hard problem, a number of simplified models have been proposed in literature to capture the essential properties of this problem. In this paper we introduce the hexagonal lattices with diagonals to handle the protein folding problem considering the well researched HP model. We give two approximation algorithms for protein folding on this lattice. Our first algorithm is a 5/3-approximation algorithm, which is based on the strategy of partitioning the entire protein sequence into two pieces. Our next algorithm is also based on partitioning approaches and improves upon the first algorithm.

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A conformation of the string PHPHPHPHPHPHPH on the lattice. In this figure, a conformation on hexagonal lattice with diagonal is illustrated.
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Figure 3: A conformation of the string PHPHPHPHPHPHPH on the lattice. In this figure, a conformation on hexagonal lattice with diagonal is illustrated.

Mentions: In an conformation, a vertex occupied by an H (P) will often be referred to as an H-vertex (a P-vertex). Figure 3 shows an example of a conformation. Throughout the paper, H-vertices are indicated by filled circle and P-vertices are indicated by blank circles.


Protein folding in HP model on hexagonal lattices with diagonals.

Shaw D, Shohidull Islam AS, Sohel Rahman M, Hasan M - BMC Bioinformatics (2014)

A conformation of the string PHPHPHPHPHPHPH on the lattice. In this figure, a conformation on hexagonal lattice with diagonal is illustrated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4016602&req=5

Figure 3: A conformation of the string PHPHPHPHPHPHPH on the lattice. In this figure, a conformation on hexagonal lattice with diagonal is illustrated.
Mentions: In an conformation, a vertex occupied by an H (P) will often be referred to as an H-vertex (a P-vertex). Figure 3 shows an example of a conformation. Throughout the paper, H-vertices are indicated by filled circle and P-vertices are indicated by blank circles.

Bottom Line: Since, this is a hard problem, a number of simplified models have been proposed in literature to capture the essential properties of this problem.In this paper we introduce the hexagonal lattices with diagonals to handle the protein folding problem considering the well researched HP model.We give two approximation algorithms for protein folding on this lattice.

View Article: PubMed Central - HTML - PubMed

ABSTRACT
Three dimensional structure prediction of a protein from its amino acid sequence, known as protein folding, is one of the most studied computational problem in bioinformatics and computational biology. Since, this is a hard problem, a number of simplified models have been proposed in literature to capture the essential properties of this problem. In this paper we introduce the hexagonal lattices with diagonals to handle the protein folding problem considering the well researched HP model. We give two approximation algorithms for protein folding on this lattice. Our first algorithm is a 5/3-approximation algorithm, which is based on the strategy of partitioning the entire protein sequence into two pieces. Our next algorithm is also based on partitioning approaches and improves upon the first algorithm.

Show MeSH