vskkl-LigandScoringProtocol.txt

Name

AutoDock Vina

Software

AutoDock Vina 1.1.2

Parameters

Autodock Vina restraints
Assumed pH 7.4

Method

We assigned protonation states and initial ligand conformations with MarvinSketch and the MMFF94 force field (100 conformers, 0.1 diversity limit). Ligands were geometry optimized in Gaussian with the AM1 semi-empirical method (VSTO-3G), followed by file preparation in Autodock Tools. The given Apo protein was protonated in Chimera, followed by preparation in Autodock Tools. Docking was conducted with Autodock Vina.

vskkl-PosePredictionProtocol.txt

Name

Bevan Lab Ranking Protocol (na

Software

MarvinSketch 16.10.31, Gaussian 09, Autodock Tools4), Autodock Vina 1.1.2, UCSF Chimera

System Preparation Parameters

MMFF94 followed by AM1 geometry, Autodock Tools ligand charges, Chimera histidine protein charges

System Preparation Method

We assigned protonation states and initial ligand conformations with MarvinSketch and the MMFF94 force field (100 conformers, 0.1 diversity limit). Ligands were geometry optimized in Gaussian with the AM1 semi-empirical method (VSTO-3G), followed by file preparation in Autodock Tools. The given Apo protein was protonated in Chimera, followed by preparation in Autodock Tools. Docking was conducted with Autodock Vina.

Pose Prediction Parameters

Autodock Vina restraints

Pose Prediction Method

Autodock Vina 1.1.2