Question: How to calculate the binding affinity of a docked complex?
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gravatar for mgab
2.2 years ago by
mgab50
Germany
mgab50 wrote:

According to the below link:

https://www.schrodinger.com/kb/573

One can compute the binding affinity of a docked complex using PRIME MMGBSA and macromodel embrace.

My questions are:

  1. There are two modes in which the Embrace calculation, that is, Energy difference mode and Interaction energy mode. Which mode should I employ?

  2. If we use embrace macromodel, which of the following embrace descriptors do we use to rank the binding affinity of the ligands that is,

Embrace_Total_Energy_without_constraints

Embrace_Valence_Energy

Embrace_vdW_Energy

Embrace_Electrostatic_Energy

Embrace_Solvation_Energy

Embrace_Constraint_Energy

Thanks

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by mgab50
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