Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice.

ABSTRACT: Lattice models of proteins have been extensively used to study protein thermodynamics, folding dynamics, and evolution. Our study considers two different hydrophobic-polar (HP) models on the 2D square lattice: the purely HP model and a model where a compactness-favoring term is added. We exhaustively enumerate all the possible structures in our models and perform the study of their corresponding folds, HP arrangements in space and shapes. The two models considered differ greatly in their numbers of structures, folds, arrangements, and shapes. Despite their differences, both lattice models have distinctive protein-like features: (1) Shapes are compact in both models, especially when a compactness-favoring energy term is added. (2) The residue composition is independent of the chain length a

SUBMITTER: Moreno-Hernandez S 

PROVIDER: S-EPMC3348970 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature