<b>Lee et al., 2024, </b><b>Reprogramming of flagellin receptor responses with surrogate ligands</b>

Schrödinger suites (ver 2021-4) was used as follows: the crystal structure of FLS2ECD (PDB ID:4MNA) was obtained from the PDB database (https://www.rcsb.org) and processed using the default settings on the Protein Preparation pipeline of the software. 5 different receptor grids (<20Å) were generated to encompass every possible binding pocket on the FLS2 structure. SMILE strings of chemicals were processed into 3D structure for docking by LigPrep. The docking was conducted using Glide XP mode, with flexible ligand setting. 10 poses for each chemical isoforms were extracted based on binding energy prediction computed with MM-GBSA. Subsequently, the lateral chains of FLS2 amino acids participating in interaction with the chemicals within a 12 Å window were extracted. All steps were conducted under simulatory pH=5.3. Visualization of the estimated model was performed using PyMOL (ver 2.5.5).