I need to study the interaction between some drugs and miRNAs. I was wondering if someone can tell me how can I perform this simulation? Is there any software? or how can I perform this simulation for a list of drugs against a list of miRNAs?
Try with SwissDock. It can be used for protein interaction and docking of small molecules related studies. You have to create an account and submit your query. The docking program takes some time.