title: Protein folding using fragment assembly and physical energy function.
abstract: We perform a systematic study of the effects of sequence-independent backbone interactions and sequence-dependent side-chain interactions on protein folding using fragment assembly and physical energy function. Structures for ten proteins belonging to various structural classes are predicted only with Lennard-Jones interaction between backbone atoms. We find nativelike structures for beta proteins, suggesting that for proteins in this class, the global tertiary structures can be determined mainly by sequence-independent backbone interactions. On the other hand, for alpha proteins, nonlocal hydrophobic side-chain interaction is also required to obtain nativelike structures.
authors.affiliation: School of General Education, ChungJu National University, Chungju 380-702, Korea.
authors.forename: Seung-Yeon
authors.initials: SY
authors.lastname: Kim
authors.forename: Weontae
authors.initials: W
authors.lastname: Lee
authors.forename: Julian
authors.initials: J
authors.lastname: Lee
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins