Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Details Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

1998-12-15

arxiv.org/abs/cond-mat/9812238v2

Phys. Rev. Lett. 84, p.386, 2000

Physics

Condensed Matter

Soft Condensed Matter

4 pages, 2 figures

Scientific paper

10.1103/PhysRevLett.84.386

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.

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