A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model

A branch and bound algorithm is proposed for the two-dimensional protein folding problem in the HP lattice model. In this algorithm, the benefit of each possible location of hydrophobic monomers is evaluated and only promising nodes are kept for further branching at each level. The proposed algorith...

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Detalles Bibliográficos
Autores principales: Chen, Mao, Huang, Wen-Qi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2005
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172541/
https://www.ncbi.nlm.nih.gov/pubmed/16689690
http://dx.doi.org/10.1016/S1672-0229(05)03031-7
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author Chen, Mao
Huang, Wen-Qi
author_facet Chen, Mao
Huang, Wen-Qi
author_sort Chen, Mao
collection PubMed
description A branch and bound algorithm is proposed for the two-dimensional protein folding problem in the HP lattice model. In this algorithm, the benefit of each possible location of hydrophobic monomers is evaluated and only promising nodes are kept for further branching at each level. The proposed algorithm is compared with other well-known methods for 10 benchmark sequences with lengths ranging from 20 to 100 monomers. The results indicate that our method is a very efficient and promising tool for the protein folding problem.
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spelling pubmed-51725412016-12-23 A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model Chen, Mao Huang, Wen-Qi Genomics Proteomics Bioinformatics Article A branch and bound algorithm is proposed for the two-dimensional protein folding problem in the HP lattice model. In this algorithm, the benefit of each possible location of hydrophobic monomers is evaluated and only promising nodes are kept for further branching at each level. The proposed algorithm is compared with other well-known methods for 10 benchmark sequences with lengths ranging from 20 to 100 monomers. The results indicate that our method is a very efficient and promising tool for the protein folding problem. Elsevier 2005 2016-11-28 /pmc/articles/PMC5172541/ /pubmed/16689690 http://dx.doi.org/10.1016/S1672-0229(05)03031-7 Text en . http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Chen, Mao
Huang, Wen-Qi
A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model
title A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model
title_full A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model
title_fullStr A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model
title_full_unstemmed A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model
title_short A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model
title_sort branch and bound algorithm for the protein folding problem in the hp lattice model
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172541/
https://www.ncbi.nlm.nih.gov/pubmed/16689690
http://dx.doi.org/10.1016/S1672-0229(05)03031-7
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