A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations.

ABSTRACT: Backbone-dependent rotamer libraries are commonly used to assign the side chain dihedral angles of amino acids when modeling protein structures. Most rotamer libraries are created by curating protein crystal structure data and using various methods to extrapolate the existing data to cover all possible backbone conformations. However, these rotamer libraries may not be suitable for modeling the structures of cyclic peptides and other constrained peptides because these molecules frequently sample backbone conformations rarely seen in the crystal structures of linear proteins. To provide backbone-dependent side chain information beyond the α-helix, β-sheet, and PPII regions, we used explicit-solvent metadynamics simulations of model dipeptides to create a new rotamer library that has high co

SUBMITTER: Mortensen JC 

PROVIDER: S-EPMC9679973 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature