I want to calculate the binding affinity of dsDNA ligand complex. Which interface of prodigy web server should i use i.e prodigy, prodigy protein ligand or prodigy crystal?
None of those support DNA. We don’t have any software for this.
@amjjbonvin mjjbovin Sir i got the results about above mentioned complexes by using prodigy protein ligand interface. That means these are not reliable?
Was never tested / benchmarked for protein-DNA…
In output folder even i got IC_List file containing information about contact residues along with stat folder. So, can we use this as a logic that prodigy protein ligand interface can be used for DNA ligand complex too?
It is giving contacts, but has never been tested for protein-DNA complexes.
No idea what the accuracy is. Use it at your own risk.