Omega/HYBRID/MM-GBSA
Omega 3.0.8/HYBRID 3.2.0.2/MM-GBSA/amber16
Assumed pH 4.5
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 1000 conformations per ligand was gerenated. Ligand protonation state was generated at pH 4.5 using pKa Plugin from ChemAxon. Pdb4amber was used to renumber the protein residues in the PDB structures with only positive integer residue numbers. 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-ligand complex was solvated in TIP3P water in a cubic box with 10 Angstrom padding.
50 docked 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
We have used the 20 BACE structures provided by the D3R Challenge to dock the ligands. 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 estimate the binding free energy. Poses generated by MD simulations were then selected based on their stability in the binding pocket and also the calculated binding energy.
Yes
Yes