[modeller_usage] Restraints to apply for nucleic acid
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Subject: [modeller_usage] Restraints to apply for nucleic acid
From: Charlotte Habegger-Polomat <>
Date: Tue, 20 Jun 2006 10:50:37 -0400
Hello!
Modeller has been quite successful at modelling my protein of interest
and I am very happy with the results. I am now using Modeller to model
my protein in complex with a nucelic acid (tNRA), as there is a homolog
complex of known structure.
The family of models I obtained is quite good but the nucleic acid
seems a little out of shape. It looks like some of the base pairing
and/or stacking has been lost.
I have been thinking of adding restraints to the modelling process.
Do you have any ideas on the best type of restraints to use (H-bonds,
distance, etc.)?
Thanks!
-Charlotte Habegger-Polomat, Quebec