Molecular Docking

The binding sites of FGFR1 with Y14 and Af23 were studied by using AutoDock (version 4.2.6) software (Morris et al., 2009). The crystallographic co-ordinates for human FGFR1 (PDB ID: 3RHX, 4UWC, 5EW8) were retrieved from the Protein Data Bank (PDB). Firstly, PyMOL software was used to remove water molecules and other ligands to prepare protein structure (Alexander et al., 2011). A grid box with a size of 60 × 60 × 60 dimensions and a spacing of 0.375 Å was set up, covering almost the entire FGFR1 binding site. All docking calculations were used the Lamarckian genetic algorithm (LGA) with 50 LGA runs. Other parameters are set by default. AutoDockTools (version 1.5.6) and PyMol was used to analyze the docking results (Morris et al., 2009).