Predicting protein stability changes upon mutation using a simple orientational potential.

ABSTRACT:

Motivation

Structure-based stability prediction upon mutation is crucial for protein engineering and design, and for understanding genetic diseases or drug resistance events. For this task, we adopted a simple residue-based orientational potential that considers only three backbone atoms, previously applied in protein modeling. Its application to stability prediction only requires parametrizing 12 amino acid-dependent weights using cross-validation strategies on a curated dataset in which we tried to reduce the mutations that belong to protein-protein or protein-ligand interfaces, extreme conditions and the alanine over-representation.

Results

Our method, called KORPM, accurately predicts mutational effects on an independent benchmark dataset, whether the wild-type or mutate

SUBMITTER: Hernandez IM 

PROVIDER: S-EPMC9850275 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature