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
Descripción
Sumario: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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