It was easy to learn the possible mutational effects for protein with so much literature available. My case becomes difficult as it happens in mitochondrial tRNA. How can I predict the effects of mutation in a tRNA in positions which are not "active sites"? For eg a mutation in a stem region of T-arm where no enzyme interacts. There are tools like Vienna RNAfold, RPI mfold server but how can I use them ? What are the parameters to check whether the mutation alters the stability of the structure or that affects the stability in nearby region etc.
We also have this situation for tRNA- if we have leu-tRNA sequence and predict tRNA from available programs we may not get the accurate structure that is published.This is not the case for protein structure, if there is homology the protein modeling tools give the most possible accurate structure!