I agree with Vikash. Here's something I wrote in a proposal a few years ago - "While others have adapted small molecule docking methods for this purpose [128], we believe that it is more appropriate to use macromolecular docking methods that enumerate all possible intermolecular configurations, such as, DOT [138-140], HEX [141], or FTDock [142]."

As you've discovered Irshad, there are not near as many tools for ssDNA and ssRNA 3D structure prediction as for proteins. I would love to hear what you find out in this project as I have not looked into this issue for a while.

Best,

Bill

Hi Irshad you can try KineFold server.

http://kinefold.curie.fr/

Thanks dear Vikas for your kind suggestion. I have tried your suggested KineFold web server. However, it seems this server is confined to 2D structure predcition of RNA/ DNA (which i did earlier by similar programme MFold Server http://mfold.rna.albany.edu/ ). Infact, i am currently looking for DNA-protein docking programme,which would predict the possible binding site of the DNA aptamer onto the target protein?

Thanks again for your prompt and kind reply to my query.

Best wishes

For DNA-Protein docking You can try HAADOCK, PARADOCK and Hex.

Thanks dear Vikas for your kind suggestion. I would surely give a try.

I agree with Vikash. Here's something I wrote in a proposal a few years ago - "While others have adapted small molecule docking methods for this purpose [128], we believe that it is more appropriate to use macromolecular docking methods that enumerate all possible intermolecular configurations, such as, DOT [138-140], HEX [141], or FTDock [142]."

As you've discovered Irshad, there are not near as many tools for ssDNA and ssRNA 3D structure prediction as for proteins. I would love to hear what you find out in this project as I have not looked into this issue for a while.

Best,

Bill

Hi Irshad,

Are you finally reached your purpose ? If it's yes, could you explain how ?

Best,

Cynthia

Thank you all for your interest. I yet did not find some concrete method to resolve this issue. Im working on it. I would ceratinly share my experiences soon i accomplished this goal.

Best,

Irshad

Hie Irshad 

Which docking program/online server did you end up using to perform your ssDNA aptamer-protein docking?

what about Hex? this is what I am using for RNA - protein docking

Hi mr Irshad i am facing the same problem but I have to do RNA and protein docking. Letizi chiodo thanks for suggestion

hi, what about aoutodock?

please guide me

Hi, everyone. If anyone came up with a solution kindly inform.

Best Regards.

I found an article that does the modeling of DNA aptamer

https://www.nature.com/articles/s41598-017-01348-5