Protein folding in HP model on hexagonal lattices with diagonals

Dipan Lal Shaw,Masud Hasan,Asm Shohidull Islam,M Sohel Rahman

doi:10.1186/1471-2105-15-s2-s7

Dipan Lal Shaw, Masud Hasan + Show 2 more

Open Access

https://doi.org/10.1186/1471-2105-15-s2-s7

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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 -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.

Highlights

Protein folding is one of the most studied computational problems in bioinformatics
We introduce the hexagonal lattices with diagonals for protein folding
Our approaches we present two approximation algorithms for protein folding in a hexagonal lattice with diagonal

Summary

Introduction

Protein folding is one of the most studied computational problems in bioinformatics. Many approximation solutions for this problem are given in the literature by using simplified, abstract models. Theorem 0.5 For any given HP string, Algorithm ChainArrangement gives a 53approximation ratio for k > 10, where k is the total number of H-runs. □. Theorem 0.6 For any given HP string, Algorithm ChainArrangement is expected to achieve an approximation ratio of 53for n ≥ 16, where n is the total number of H. As will be discussed later, the better approximation ratio will be applicable only if every H-run is of length greater than 2 For this improved algorithm we introduce the notion of inner-left chains,. Rest of the H’s of the H-run are placed alternatively on the inner-left chain (inner-right chain) and on the outer-left chain (outer-right chain) (see Figure 10) At this point, a brief discussion on the difference between the arrangements done by the two algorithm is in order.

Suppose F denotes the position in p after the f-th

Conclusion

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