Computational protocol: The cytotoxicity of BAMLET complexes is due to oleic acid and independent of the α-lactalbumin component

Similar protocols

Protocol publication

[…] YASARA software was used to perform all the calculations. The BAMLET complex model was created using the apo bovine α-LA (1F6R) and 6 molecules of OA (4DQ3) from RCSB Protein Data Bank. The system was pre-equilibrated by the steepest descent minimization using AMBER03 force field at 25 °C with a cutoff of 7.86431 Å. The BAMLET model was solvated in a cubic box with the size of 20 Å and filled with explicit water molecules (0.997 g/ml of density and 1.4 Å of radius). Periodic boundary conditions were applied in all directions and the system was neutralized by adding counter ions replacing the water molecules. The energy-minimized system was subjected to 50 ps of equilibration. The docking calculations were carried out using AutoDock 4.2 to compute the free energy of binding (Docking runs = 50; Cluster RMSD = 5.00 Å) . Five different docking jobs were run using initial positions, orientation and torsions of the ligand moieties randomly set. The final structure with all the ligand moieties bound to the potential binding sites was further refined by simulated annealing minimization using the following conditions: AMBER03, 60 °C, cutoff of 7.86431 Å, same solvated cubic box dimension and conditions. […]

Pipeline specifications

Software tools YASARA, AutoDock
Applications Drug design, Protein interaction analysis
Organisms Homo sapiens, Bos taurus
Diseases Amino Acid Metabolism, Inborn Errors, Neoplasms, Drug-Related Side Effects and Adverse Reactions