Dear Sir,
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.
Thank you,
Sincerely,
Irshad Baig
irshad@hanyang.ac.kr
I've forwarded your question to someone who may be able to help.
-J
Hi Irshad,
This is from Phil Bradley, who has done a lot with Rosetta and DNA - sorry it's not the great news you were hoping for:
That sounds really hard. His best bet with Rosetta would be to pretend it is RNA, fold with Rhiju's RNA folding code which is in trunk and very well documented, and see if the structure also makes sense as DNA. We haven't done anything at all with ssDNA.
-J
If I knew more about RNA code I would help you with that as well, but I also have no experience there...