I have a DNA sequence which has predictability to form G quadruplex . I need a software to generate a pdb of it which will form G quadruplex. I am using open Babel but I am not able to set the coordinates.
Dear Pallavi Agrawal,
fortunately yes and I use it a lot: 3D-NuS webserver by Indian Institute of Technology Hyderabad (https://iith.ac.in/3dnus/Quadruplex.html). To the best of my knowledge, this is the only user-friendly G4 sequence ->structure modeling tool.
Hope this help,
Martin
Martin Bartas How could i do enrgy minimisation of these generated pdb structures.
I have tried yasara but it is not saving my output pdb file.
Pallavi Agrawal, have you tried to contact the YASARA team?
http://www.yasara.org/contact.htm
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@Martin Bartas yes I have mail to them but they have not replied yet.
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