Re: The best initial structure of Protein-Protein complex

Date: Mon Feb 24 2020 - 09:54:28 CST

Hi Alireza,

you can use HADDOCK, actually is el best program for make docking
protein-protein. Also is suggest that you use any type of restriction for
your docking, for get best pose.

El lun., 24 de feb. de 2020 a la(s) 05:21, Alireza Mansouri ( escribió:

> Dear NAMD users,
> I would like to research on the interaction between two proteins using MD
> Simulation. However, I do not know what the best way is to obtain the
> initial structure of protein/protein complex before simulation. As far as I
> know, there are some docking web servers and software like Hex8, which can
> be used for this work. I did some docking simulations and found that each
> software or server provided different result (different proteins
> orientation).
> Can anyone please offer me some advice?
> Can I use the result of Hex 8 for my MD Simulation?
> Thanks in advance
> Alireza


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