I want to study the dynamics of ABC transporters along with a peptide molecule which in physiological conditions passes through the transporter. I am clueless how to set the peptide molecule in to the system so that it pass through the transporter. Should i go ahead and dock it first and then run the simulation?
I am using Desmond for simulations.
Thanks in advance
In my Opinion, You can use Steered molecular dynamics in order to facilitate and study transportation of component via channels.
I encourage you to read aquaporin SMD studies.
Also online talks by Prof. Tajkhorshid may help you to have a new perspectives in this field.
here is one of the articles and you can find more:
Article What Makes an Aquaporin a Glycerol Channel? A Comparative St...
Since this might a very rare event, a single MD will probably not capture it without some pre-positioning and maybe even guiding (pulling), imo.
In my Opinion, You can use Steered molecular dynamics in order to facilitate and study transportation of component via channels.
I encourage you to read aquaporin SMD studies.
Also online talks by Prof. Tajkhorshid may help you to have a new perspectives in this field.
here is one of the articles and you can find more:
Article What Makes an Aquaporin a Glycerol Channel? A Comparative St...
I agree with Geist, randomly placing the molecule near the protein will probably not give you the results you are looking for.
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