This section describes the computational strategy used to identify and characterize microbial peptide candidates capable of mimicking a human self-peptide in binding to HLA-B27:05.
The workflow consists of five major stages:
Data Preparation, including:
a. Selection of data sources
b. Peptide generation and extraction, comprising:
i. Peptide slicing
ii. Peptide filtering and molecular mimicry screening
Molecular Docking and Selection of Peptides
Molecular Dynamics Simulations
Post-Trajectory Correction and Processing
Post-MD Trajectory Analysis
The overview of the Pipeline is shown in Figure 1 and the detailed methods are presented in the next part.
Figure 1:Overview of the workflow used in this study