How to deal or explain multiple conformations at binding interface of protein complex ?

Srinivasa Rao Penumutchu @Srinivasa_Penumutchu

01 January 2014 1 8K Report

I finished docking based on NMR data and MD simulations using Gromacs . I would like to know that What kind of data should be provide from simulations to explain or confirm the multiple conformation at binding interface of protein complex ?

Yun Shi

The mere fact that you have multiple conformations during MD simulations?

Why not you do some clustering using GROMACS and see if you have more than one cluster (populated based on your criteria) that show binding of your protein complex.

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