mhswo-FreeEnergyProtocol.txt

Name

DelPhi-Gaussian Dielectric MM/PBSA

Software

Medusa 1.1/Delphi 7.1/NAMD 2.11/Amber 14/Gaussian 09/VMD 1.9.3

Parameters

Assumed pH 7
Minimize 5000
Nonlinear PB at salt 0.15

Method

We used Gaussian 09 to calculate charge, bond, and other parameters for Amber force field.
Assumed pH of 7. The top 100 poses found by Medusa docking were energy minized for 5000 steps using
NAMD. PB energies are given by DelPhi. SASA is given by VMD. The MMM/PBSA energies are Boltzmann
averaged. The average energy is used as the score. See the following publications for the details in the method.
*Li L, Li C, Zhang Z, Alexov E.; "On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi"; J Chem Theory Comput. 2013 Apr 9;9(4):2126-2136.
*Jia Z, Li L, Chakravorty A, Alexov E. "Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi." J Comput Chem. 2017 Aug 15;38(22):1974-1979.

mhswo-PosePredictionProtocol.txt

Name

Medusa-Dock

Software

Medusa-Dock 1.1

System Preparation Parameters

Assumed pH 7
Flexible docking
Medusa FF

System Preparation Method

1. Add missing heavy atoms and hydrogen: Medusa-reconstruction, Medusa force field.
2. Flexible docking: all protein side chains near the pocket and the ligand are considered as flexible.
See details in the following publications:
*F. Ding, Yin, S., and Dokholyan, N. V. “Rapid flexible docking using a stochastic rotamer library of ligands”, Journal of Chemical Information and Modeling, 50:1623-32 (2010)
*F. Ding and N.V. Dokholyan, “Incorporating backbone flexibility in MedusaDock improves ligand binding pose prediction in the CSAR2011 docking benchmark”, J. Chem. Inf. Model., 53:1871-1879 (2013)

Pose Prediction Parameters

Flexible docking.
poses within 2.5A cut-off are considered to be in a cluster.
The lowest energy poses of the top 5 clusters are submitted as the prediction.

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 MM/PBSA scoring are submitted with this protocol.

Answer 1

No