Question: How to calculate the binding affinity of a docked complex?
0
gravatar for mgab
18 months ago by
mgab40
Germany
mgab40 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 18 months ago • written 18 months ago by mgab40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1914 users visited in the last hour