I would like to predict the 3D structure of ssDNA aptamer sequence but I cant find any tool for DNA 3D structure prediction, but only available for RNA. Several articles mentioned to convert the DNA 2D structure to 3D RNA first then convert back to DNA. Is there any detailed protocol on the conversion of RNA-DNA, I have no idea on the procedures? Or is there any tools available for ssDNA 3D structure modeling? Thanks in advance.
. using alpha fold3 (https://alphafoldserver.com/welcome), 3dna rna (http://biophy.hust.edu.cn/new/3dRNA/create) server you can generate DNA or RNA , also try to use avogadro software , be aware that choosing software is depend on your aim of work
for rna aptamer its best to use RNA composer
https://rnacomposer.cs.put.poznan.pl/;jsessionid=9D1B795A02A04B9D032464EAFA5380C8
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