Hello!. I am Irshad Baig, pursuing PhD in Biochemistry.
I am writing you to seek your help regarding 3D structure prediction of ss DNA and ssDNA-Protein docking studies.
Infact, I am trying to build 3D model structure for my ss DNA aptamer, as i am further interested to study DNA -protein interaction through docking. However, I did not succeed in building 3D struture for ss DNA aptamer.
Trying one reccommended programme,i could able to built 3 D model for ss DNA,however it is in the 'B' form of DNA,however i need 3 D model of ss DNA in the native stem/loop form. Further, I have predicted secondary structures of my ssDNA aptamers by Mfold programme, however I did not find any modeling programme to predict tertiary (3D) structure of a DNA, thus would generate PDB/PDBQT file of the DNA aptamers that would be further helpful to study DNA-Protein docking, i assume.
Therefore, I would highly appreciate, if you could please extend me your valuable guidance/suggestions to perform 3D structure prediction of ss DNA aptamer and ss DNA aptamer-Protein docking.
Should you need any information, please do let me know.
Looking forward for your kind suggestions to resolve this issue.