8h4d2-LigandScoringProtocol.txt

Name

AlGDock

Software

OpenEye QUACPAC
modeller 9.18
UCSF dock6
AmberTools 14
NAMD 2.9

Parameters

binding site max radius 6 Å
High temperature 600k
Low temperature 300K
cooling 10 cycles
docking 17 cycles
Each cycle consists of 1000 iterations of Hamiltonian Monte Carlo
NAMD OBC solvent model

Method

In AlGDock based on Implicit Ligand Theory(Minh, 2012), receptor only need to calculate once, and only ligands need simulation. It’s basically made up by two parts, cooling and docking. In both processes, only the ligand molecule is flexible. With cooling, the temperature of the system (only ligand) is progressively changed from 600k to 300k. With docking, receptor-ligand interactions are models by interpolating a precomputed 3D grid. The process consists of reducing the temperature and scaling the strength of the interaction grid from 0 to 1.

Answer 1

No

8h4d2-PosePredictionProtocol.txt

Name

AlGDock

Software

OpenEye QUACPAC
modeller 9.18
UCSF dock6
AmberTools 14
NAMD 2.9

System Preparation Parameters

ligand: omega.SetMaxConfs(800), SetEnergyWindow(15.0), SetRMSThreshold(1.0), DOCK6: dotlim = 0.0, radmax = 4.0 Å, radmin = 1.4 Å, 5000 maximum orientations, minimum anchor size of 40, pruning with clustering, 1000 maximum orientations, conformer score cutoff 25, max_bumps_anchor 12, max_bumps_growth 12, RMSD threshold 2 Å. Protein topology parameters: Amber14 leaprc.ff14SB. Ligand topology parameters: Amber14 leaprc.gaff

System Preparation Method

1, 3D models of ligands with proton and charged were built by OpenEye QUACPAC , and three representative crystal protein structures (according to the RMSD of heavy atoms surrounding the binding site) plus two structures provided by G3R were run homology model by modeller-9.18 and generated sphere, grids by UCSF DOCK6. 2, ligands were docked to the protein structures by using UCSF DOCK6.

Pose Prediction Parameters

binding site max radius 6 Å, High temperature 600k, Low temperature 300K,replica exchange cycles: cooling 10, docking 17. Each cycle consists of 1000 iterations of Hamiltonian Monte Carlo. Hamiltonian Monte Carlo moves consist of initializing velocities from the Maxwell-Boltzmann distribution, 50 steps of velocity Verlet using a time step of 2.0 fs. Post processed with NAMD OBC solvent models.

Pose Prediction Method

In AlGDock based on Implicit Ligand Theory(Minh, 2012), receptor only need to calculate once, and only ligands need simulation. It’s basically made up by two parts, cooling and docking. In both processes, only the ligand molecule is flexible. With cooling, the temperature of the system (only ligand) is progressively changed from 600k to 300k. With docking, receptor-ligand interactions are models by interpolating a precomputed 3D grid. The process consists of reducing the temperature and scaling the strength of the interaction grid from 0 to 1.During sampling, the ligand was treated as either desolvated or fully solvated. The consensus pose is based on the lower BPMF.

Answer 1

No

Answer 2

Yes