fibez-PosePredictionProtocol.txt

Name

Maestro/MGLTools/Autodock Vina

Software

Maestro/MGLTools/Autodock Vina Method 1

System Preparation Parameters

Assumed pH from 5 to 7
Tautomers considered
Gasteiger charges

System Preparation Method

We used Maestro for generating 3D structures in mol2 format of the ligands from their smile format with considering all possible protonation and chirality.
Thi pdbqt format of the ligands which will be used as input for ligands in Autodock Vina docking were prepared by MGLTools from their mol2 format and keeping their charge information.
The protein was added missing Hydrogen and side chain atoms by using Ambertools. The input file of the receptor for the docking was prepared by MGLTools.
We do sequence searching for receptor in PDB databank to find the similar protein structures containing ligand binding information
and we found 20 structures (with pdb ID: 1ms6, 1npz, 1nqc, 2f1g, 2h7j, 2hhn, 2hxz, 2op3, 2r9m, 2r9n, 2r9o, 3iej, 3kwn, 3mpe, 3mpf, 3n3g, 3n4c, 3ovx, 4p6e and 4p6g)
having larger than 95% sequence similarity to the provided structure. The 20 structures were aligned to CatS_SO4_structure_D3R_GC3.pdb structure.
The all the ligands coordinates of the aligned structures were gathered for docking box information.
The docking reactangel box was chosen with the minimum distance between any atoms of the aligned ligands to the box's walls is larger than 8 angstrong.

Pose Prediction Parameters

Iterated Local Search global optimizer search method
Exhaustiveness=150 #exhaustiveness of global search (default=8)
Vina scoring funtion (empirical + knowledge-based function)
Num_modes=20 #max number of poses to generate
Energy_range=7 #energy difference (kcal/mol) between the best and worst binding mode

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. The top 5 poses from the Vina docking are submitted with this protocol.

Answer 1

No

Answer 2

Yes