rofmu-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: pocket residue sample sub-rotamer conformation of the native rotamer
3. Water in crystal structure: not included
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