Molecular Docking of Dectin-1 Ligands

Centre of the active site of Dectin-1 was determined from the X, Y and Z coordinates of the active site amino acids, obtained from the.pdb file of the crystal structure. A spatial grid-box was generated using Autogrid 4.2.6 around the centre, taking 80 points in each dimension with 0.5 Å spacing. Dockings were performed according to the Genetic algorithm with 30 runs for each ligand in AutoDock 4.2.6 (Scripps Research, La Jolla, CA, USA). The Lamarckian GA (4.2) outcomes of docked complexes were analyzed and the ones with the lowest binding free energy values were taken (with.pdbqt extensions) as the most stable conformations for each ligand-receptor docked complex. The individual root mean square deviations (RMSDs), binding energies (Kcal/mol) and inhibition constants (K_i) for each ligand (with Dectin-1) were found in the respective Docking log files and the numbers of generated H-bonds along with the amino acids of Dectin-1, involved in each interaction was obtained using BIOVIA Discovery Studio Visualizer (Dassault Systemes, Île-de-France, France). All diagrams, representing the molecular interactions were prepared in BIOVIA Discovery Studio Visualizer.