normal intrinsically disordered protein

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1 month 1 week ago #7460 by dariush
dariush created the topic: intrinsically disordered protein
Hello,

Can I use MARTINI to model intrinsically disordered protein? I am thinking of using the old version of protein model without the elastic network. I would appreciate your thoughts.

Thanks!
Dariush

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1 month 1 week ago #7461 by peterkroon
peterkroon replied the topic: intrinsically disordered protein
Hi Dariush,

yes, but you will not see a change in secondary structure. In other words, a coil will *not* fold into a helix or beta-sheet. It depends on your specific system whether that is a problem.

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1 month 1 week ago #7462 by dariush
dariush replied the topic: intrinsically disordered protein
Thanks!
From your response, I learned that I should start to form a coil structure and it stays as a coil to the end, which is what I want.
Is there any publication that used MARTINI for a disordered protein?

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1 month 1 week ago #7463 by peterkroon
peterkroon replied the topic: intrinsically disordered protein
Probably, but I can't point you to a specific one.

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