On simplified global nonlinear function for fitness landscape: a case study of inverse protein folding.

ABSTRACT: The construction of fitness landscape has broad implication in understanding molecular evolution, cellular epigenetic state, and protein structures. We studied the problem of constructing fitness landscape of inverse protein folding or protein design, with the aim to generate amino acid sequences that would fold into an a priori determined structural fold which would enable engineering novel or enhanced biochemistry. For this task, an effective fitness function should allow identification of correct sequences that would fold into the desired structure. In this study, we showed that nonlinear fitness function for protein design can be constructed using a rectangular kernel with a basis set of proteins and decoys chosen a priori. The full landscape for a large number of protein folds can be

SUBMITTER: Xu Y 

PROVIDER: S-EPMC4128808 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature