Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model.

ABSTRACT: The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural stability of their affected proteins, information from structural change caused by genetic variants can be used to identify the variants with deleterious effects. In order to measure the structural change for proteins with large size, we designed a method named RP-MDS composed of Ramachandran plot (RP) and Molecular Dynamics Simulation (MDS). Ramachandran plot captures the variant-caused secondary structural change, whereas MDS provides a quantitative measure for the variant-

SUBMITTER: Tam B 

PROVIDER: S-EPMC7744649 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature