Messages

1

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« on: February 27, 2025, 11:24:32 pm »

Hi Dr. Jun,

Sorry for the late reply. Yes, I definitely think the idea in the FAQ is relevant. But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

2

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« on: January 30, 2025, 06:38:05 pm »

Hello Dr. Jun,

Thank you so much for your reply. So, my intention is to conduct an all-atom intrinsically disordered protein - ssDNA phase separation simulation using the OpenMM MD suite. I was wondering how to generate the PDB for a custom DNA sequence that contains the (m3C) modification on one of the bases.

Best,
Sunera

3

General discussions (Q&As) / Generation of ssDNA PDB with m3C modification using 3DNA webserver

« on: January 30, 2025, 12:51:31 am »

Is it possible to generate a PDB of a single stranded DNA containing a 3-methylated cytosine using the 3DNA Web Server? Could you please advise on the best way to generate an all-atom PDB containing this modification if it cannot be generated using 3DNA?