Limitations of the ABEGO-based backbone design: ambiguity between αα-corner and αα-hairpin.

ABSTRACT: ABEGO is a coarse-grained representation for poly-peptide backbone dihedral angles. The Ramachandran map is divided into four segments denoted as A, B, E, and G to represent the local conformation of poly-peptide chains in the character strings. Although the ABEGO representation is widely used in backbone building simulation for de novo protein design, it cannot capture minor differences in backbone dihedral angles, which potentially leads to ambiguity between two structurally distinct fragments. Here, I show a nontrivial example of two local motifs that could not be distinguished by their ABEGO representations. I found that two well-known local motifs αα-hairpins and αα-corners are both represented as α-GBB-α and thus indistinguishable in the ABEGO representation, although they show disti

SUBMITTER: Sakuma K 

PROVIDER: S-EPMC8214924 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature