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Folding Lattice HP Model of Proteins Using the Bond‐Fluctuation Model
Author(s) -
Zhang Linxi,
Zhao Delu
Publication year - 2001
Publication title -
macromolecular theory and simulations
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.37
H-Index - 56
eISSN - 1521-3919
pISSN - 1022-1344
DOI - 10.1002/1521-3919(20010601)10:5<518::aid-mats518>3.0.co;2-g
Subject(s) - lattice protein , lattice (music) , lattice model (finance) , degeneracy (biology) , protein folding , chemistry , ground state , native state , constraint (computer aided design) , bond length , statistical physics , folding (dsp implementation) , chemical physics , crystallography , physics , crystal structure , atomic physics , mathematics , geometry , bioinformatics , biochemistry , organic chemistry , acoustics , electrical engineering , biology , engineering , polymer
In this paper, we find ‘good’ amino acid sequences that fold to a desired “target” structure as a ground state conformation of lowest accessible free energy using the modified bond‐fluctuation lattice model. In our protein lattice model, bond lengths are set to vary between one and √2 in three dimensions. Our results agree well with the native state energies E N . Comparisons with the “putative native state” (PNS) energy E PNS and the “hydrophobic zippers” (HZ) energy E HZ are made. For every sequence, the global energy minimum is found to have multiple degeneracy of conformations, which is the same result as for the constraint‐based hydrophobic core construction (CHCC) method. The interior conformations of the ground states are also discussed.