On the protein folding problem in 2D-triangular lattices

In this paper, we present a novel approximation algorithm to solve the protein folding problem in HP model. Our algorithm is polynomial in terms of the length of the given HP string. The expected approximation ratio of our algorithm is [Formula: see text] for n ≥ 6, where n(2) is the total number of...

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Detalles Bibliográficos
Autores principales: Md Sohidull Islam, Abu Sayed, Rahman, Mohammad Sohel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Research
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175104/
https://www.ncbi.nlm.nih.gov/pubmed/24279437
http://dx.doi.org/10.1186/1748-7188-8-30
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author Md Sohidull Islam, Abu Sayed
Rahman, Mohammad Sohel
author_facet Md Sohidull Islam, Abu Sayed
Rahman, Mohammad Sohel
author_sort Md Sohidull Islam, Abu Sayed
collection PubMed
description In this paper, we present a novel approximation algorithm to solve the protein folding problem in HP model. Our algorithm is polynomial in terms of the length of the given HP string. The expected approximation ratio of our algorithm is [Formula: see text] for n ≥ 6, where n(2) is the total number of H’s in a given HP string. The expected approximation ratio tends to reach 1 for large values of n. Hence our algorithm is expected to perform very well for larger HP strings.
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spelling pubmed-41751042014-10-23 On the protein folding problem in 2D-triangular lattices Md Sohidull Islam, Abu Sayed Rahman, Mohammad Sohel Algorithms Mol Biol Research In this paper, we present a novel approximation algorithm to solve the protein folding problem in HP model. Our algorithm is polynomial in terms of the length of the given HP string. The expected approximation ratio of our algorithm is [Formula: see text] for n ≥ 6, where n(2) is the total number of H’s in a given HP string. The expected approximation ratio tends to reach 1 for large values of n. Hence our algorithm is expected to perform very well for larger HP strings. BioMed Central 2013-11-26 /pmc/articles/PMC4175104/ /pubmed/24279437 http://dx.doi.org/10.1186/1748-7188-8-30 Text en Copyright © 2013 Islam and Rahman; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Md Sohidull Islam, Abu Sayed
Rahman, Mohammad Sohel
On the protein folding problem in 2D-triangular lattices
title On the protein folding problem in 2D-triangular lattices
title_full On the protein folding problem in 2D-triangular lattices
title_fullStr On the protein folding problem in 2D-triangular lattices
title_full_unstemmed On the protein folding problem in 2D-triangular lattices
title_short On the protein folding problem in 2D-triangular lattices
title_sort on the protein folding problem in 2d-triangular lattices
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175104/
https://www.ncbi.nlm.nih.gov/pubmed/24279437
http://dx.doi.org/10.1186/1748-7188-8-30
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