A distance geometry-based description and validation of protein main-chain conformation.

ABSTRACT: Understanding the protein main-chain conformational space forms the basis for the modelling of protein structures and for the validation of models derived from structural biology techniques. Presented here is a novel idea for a three-dimensional distance geometry-based metric to account for the fine details of protein backbone conformations. The metrics are computed for dipeptide units, defined as blocks of C^α_i-1-O _i-1-C^α_i -O _i -C^α_i+1 atoms, by obtaining the eigenvalues of their Euclidean distance matrices. These were computed for ∼1.3 million dipeptide units collected from nonredundant good-quality structures in the Protein Data Bank and subjected to principal compone

SUBMITTER: Pereira J 

PROVIDER: S-EPMC5619857 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature