Omega/HYBRID/MM-GBSA
Omega 3.0.8/HYBRID 3.2.0.2/MM-GBSA/amber16
Assumed pH 7.4
Tautomers considered only for BACE_5
AM1-BCC charges
0.1 M NaCl solution for MD simulations
Amberff99sb, TIP3P and Gaff for MD simulations
Ligand conformations for shape similarity search were generated using Omega in Openeye Toolkits. A maximum number of 100 conformations per ligand was gerenated. Ligand protonation state was generated at pH 4.5 using pKa Plugin from ChemAxon. Pdbfixer was used to remove the ligand and the water molecules and to add the missing heavy atoms to the pdb structures of the receptors. Then, PDB2PQR server (http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/) was used to correct the protonation states at pH 4.5 and to fix the residue/atom names following AMBER naming scheme. Parmed was used to convert the resulting pqr file to a pdb file. OpenEye toolkits were used to check bond-order and connectivities. For MM-GBSA calculations, the protein and ligand was solvated in TIP3P water with Amberff99sb force field and solvate in a cubic box wth 10 Angstrom padding.
50 docker poses in Hybrid
OESearchResolution_High 1.0
For tleap, set default PBRadii mbondi3
Amber parameter, dt=0.002,ntc=2,ntf=2,cut=8.0, ntb=2, ntp=1, taup=2.0, ntt=3, gamma_ln=2.0, temp0=300.0
For mmgbsa calculations using MMPBSA.py, igb=8, saltcon=0.100
RCSB database was searched for similar ligands and target protein structures were selected accordingly to dock the ligand. 50 poses per ligand were generated with a high docking resolution using HYBRID, followed by optimization. Then, the docked poses were visually inspected based on the similar/reference ligand from the pdb database and similar poses were selected for the next step. The selected poses were minimized and simulated for 15 ns using explicit solvent MD simulations in NPT ensemble and the MM-GBSA calculations were performed on the last 10 ns to estimated the binding free energy. Ligands were then selected based on their stability in the binding pocket and also the calculated binding energy.
Yes
Yes
Chimera/Omega/HYBRID/MM-GBSA
Amber18 for MD, Amber16 for MMPBSA.py
For tleap, set default PBRadii mbondi3
Amber parameter, dt=0.002,ntc=2,ntf=2,cut=8.0, ntb=2, ntp=1, taup=2.0, ntt=3, gamma_ln=2.0, temp0=300.0
For mmgbsa calculations using MMPBSA.py, igb=8, saltcon=0.100
The ligand, water and the ions were first minimized for 1000 steps keeping the protein fixed using 25 and 10 kcal/mol-Ang^2 positional restraints respectively. The system was then heated from 10 K to 300 K in NVT ensemble for 140 ps while restraining the protein-ligand complex using positional restraints of 10 kcal/mol-Ang^2. Next, the restraints were gradually released using 5 and 2 kcal/mol-Ang^2 restraints on the protein-ligand complex for 20 ps, and then 2 kcal/mol-Ang^2 restraint only on the ligand for 20 ps. The temperature was regulated in the NVT simulations through Langevin dynamics with a collision frequency of 2 ps-1. The production run was performed in NPT ensemble for 14 ns with the first 4 ns being discarded as equilibration. Constant pressure was maintained in the simulation using isotropic pressure scaling with a relaxation time of 2 ps. The MMPBSA.py program was used to calculate the absolute protein-ligand binding free energy using the GBneck2 model with a salt concentration of 0.1 nM.
Yes
No