1479-1-a08gh-PosePredictionProtocol.txt

Name

Omega/HYBRID/MM-GBSA

Software

Omega 3.0.8/HYBRID 3.2.0.2/MM-GBSA/amber16

System Preparation Parameters

Assumed pH 4.5
AM1-BCC charges
0.1 M NaCl solution for MD simulations
Amberff99sb, TIP3P and GAFF2 for MD simulations

System Preparation Method

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.

Pose Prediction Parameters

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

Pose Prediction Method

We chose a reference ligand based on the closest structure from the 20 PDB structures provided by the D3R Challenge. We assumed that the compounds are going to bind in a similar way to the reference ligand, and made the neccessary changes to transform the reference ligand into the ligands using Chimera. If the changes were difficult like breaking macrocycle or non-aromatic rings, we used combination of Omega/Hybrid and visual inspection to pick the poses. Then the poses were minimized and simulated for 14 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.

Answer 1

Yes

Answer 2

Yes

1479-2-s5y65-LigandScoringProtocol.txt

Name

Chimera/Omega/HYBRID/MM-GBSA

Software

Chimera/Omega 3.0.8/HYBRID 3.2.0.2/MM-GBSA/amber16

Parameters

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 used MMPBSA.py, istrng=0.100

Method

We chose a reference ligand based on the closest structure from the 20 PDB structures released in stage 1-b. We assumed that the compounds are going to bind in a similar way to the reference ligand, and made neccessary changes to transform the reference ligand into the ligands in the scoring challenge using Chimera. If the changes were difficult like breaking macrocycle or non-aromatic rings, we uses combination of Omega/Hybrid and visual inspection to pick poses as we did in the pose prediction challenge. The protein-ligand structure was then minimized and simulated for 14 ns using explicit solvent MD simulations in NPT ensemble. In the final step, MM-GBSA calculations were performed on the last 10 ns to estimated the binding free energy.

Answer 1

Yes

Answer 2

No