Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders.

ABSTRACT: The prediction of peptide binders to Major Histocompatibility Complex (MHC) class II receptors is of great interest to study autoimmune diseases and for vaccine development. Most approaches predict the affinities using sequence-based models trained on experimental data and multiple alignments from known peptide substrates. However, detecting activity differences caused by single-point mutations is a challenging task. In this work, we used interactions calculated from simulations to build scoring matrices for quickly estimating binding differences by single-point mutations. We modelled a set of 837 peptides bound to an MHC class II allele, and optimized the sampling of the conformations using the Rosetta backrub method by comparing the results to molecular dynamics simulations. From the dyn

SUBMITTER: Ochoa R 

PROVIDER: S-EPMC8253603 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature