Medusa-Dock
Medusa-Dock 1.1
Assumed pH 5
Flexible docking
Medusa FF
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)
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.
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.
No