Hello good people, I'm trying to do a simulation with my siRNA (as a ligand) and Ago-2 protein. I build my siRNA structure using mFOLD, RNAComposer, and the protein using the Swiss model webserver. Also, I've performed the simulation in Desmond. However, the problem has been arising after loading the output file. There is no ligand with protein in the result pdf. What do you think I should do now? Please help me.
Hi,
When you load the analysis of the simulation data with the Simulation Interacion Diagram application, the software will open the SID Analsis Setup window. Here, by default, Auto is selected for Protein and Ligand selection. You can leave the Protein selection as Auto. To see your siRNA, you must change the Ligand selection and select the structure you want to analyse. To do this, change the Auto setting of Ligand to Select ASL. The software will open a window and ask you to manually select your ligand. There are several tabs at the top of the window. From these tabs you can select your siRNA (if you actually included it in the simulation) and have it analysed.
- Badges
- Science method
- Similar topics
- Mathematics
- Statistics
- Statistical Techniques
- Meta-Analysis