Data for: Molecular docking simulation of FMP or N-FMP and FAPα

The data proves that a longer self-immolative linker of FMP improves the probe responsivity toward FAPα. To uncover the underlying mechanism, theoretical molecular docking simulation is further carried out to elucidate the different FAPα responsivity towards FMP and N-FMP by MolAICal 1.3. The X-ray crystal structure of FAPα from the Protein Data Bank (PDB code 1Z68) is used. 3D structures of FMP and N-FMP are obtained and energetically optimized by a ChemDraw 3D software. After molecular docking, FMP presents a strong hydrogen bond between the peptide substrate of the probe and FAPα residues at the site of Val540, Ser548, Gln547, Gly542, and Ser546 in the active pocket. By contrast, N-FMP shows relatively weak hydrogen bond interaction with only one site of FAPα at the Gln547 residue in the active pocket. The theoretical simulations indicate that the higher affinity of FAPα towards FMP and thus promotes the enzymatic cleavage efficiency relative to N-FMP, which is consistent well with t..., 1.5 Docking Analysis. The X-ray structure of FAPα (PDB code 1Z68) is obtained from the Protein following Data Bank (http://www.rcsb.org/pdb). 3D structures of FMP and N-FMP are obtained and energetically optimized by ChemDraw 3D software. The MolAICal software package is used to process and save FAPα, FMP, and N-FMP in PDBQT molecular format. FAPα is the definition of a crystal ligand in the active pocket of molecular docking. Take x = 39.84 Å, y = 0.221 Å, and z = 59.383 Å as the center coordinate of the FAPα active pocket box, and the size of the grid box is set to 30 Å. The detained operations are as follows:
1.5.1 Software Requirement
1) MolAICal: https://molaical.github.io
2) UCSF Chimera: https://www.cgl.ucsf.edu/chimera
1.5.2 Prepare the Receptor Protein
The X-ray structure of FAPα (PDB code 1Z68) was obtained from the protein following data bank (http://www.rcsb.org/pdb). Save the file in 1Z68.pdb format.
1.5.3 Prepare the Ligand Molecule
3D structures of FMP and N-FMP are obta...,  Software requirement
1) MolAICal: https://molaical.github.io
2) UCSF Chimera: https://www.cgl.ucsf.edu/chimera