Dear Dhiraj,
I believe the solution is using combination of our dnatco.datmos.org
description of nucleic acid conformations (so called NtC) and the MMB
(MacroMoleculeBuilder, the github version implements NtC modeling). Contact me
if you need more details.
best,
JC
On 01. 01. 22 18:38, Srivastava, Dhiraj wrote:
Thank for the suggestion.
I think I should have been more specific about the problem. The promoter has
binding site for two different transcription factors which interacts with each
other to affect the transcription in spatiotemporal manner. I solved the
structure of one protein (not deposited in PDB yet) which shows DNA bending. I
am curious to see how this DNA bending affect the conformation of DNA nearby
thus potentially affecting the binding of other transcription factor through
DNA mediated allosterism. Off-course I am going to do simulation after
extending the DNA. Since DNA is bend, I can not simply extend it using ideal
DNA double helix conformation. How can I extend it computationally? x3DNA will
work but needs pdb id.
Thanks
Dhiraj
From: Phoebe A. Rice <mailto:pr...@uchicago.edu>
Sent: Saturday, January 1, 2022 11:01 AM
To: Srivastava, Dhiraj <mailto:dhiraj-srivast...@uiowa.edu>;
CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [External] Re: [ccp4bb] protein DNA complex structure and extension of
DNA structure
I would try the tools on this site - http://web.x3dna.org/index.php/protein
From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of
"Srivastava, Dhiraj" <mailto:dhiraj-srivast...@uiowa.edu>
Reply-To: "Srivastava, Dhiraj"
<mailto:dhiraj-srivast...@uiowa.edu>
Date: Monday, December 27, 2021 at 8:32 PM
To: "CCP4BB@JISCMAIL.AC.UK"<mailto:CCP4BB@JISCMAIL.AC.UK>
<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] protein DNA complex structure and extension of DNA structure
Hi
I solved the structure of protein DNA complex where the DNA molecule is
bent. I want to extend the DNA computationally so I can model two DNA binding
proteins together on same DNA molecule. is there a way by which I can extend
the DNA in both direction? its easy to do it with ideal DNA molecule but I
don't know how to do it with bent DNA.
Thank you
Dhiraj
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