title: Mean-field HP model, designability and alpha-helices in protein structures.
abstract: Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with a large number of switchbacks 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.
authors.affiliation: National Center for High-Performance Computing, Hsinchu, Taiwan, Republic of China.
authors.forename: C T
authors.initials: CT
authors.lastname: Shih
authors.forename: Z Y
authors.initials: ZY
authors.lastname: Su
authors.forename: J F
authors.initials: JF
authors.lastname: Gwan
authors.forename: B L
authors.initials: BL
authors.lastname: Hao
authors.forename: C H
authors.initials: CH
authors.lastname: Hsieh
authors.forename: H C
authors.initials: HC
authors.lastname: Lee
mesh_terms: D003198:Computer Simulation; D016208:Databases, Factual; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D010455:Peptides; D011506:Proteins