I have been using HADDOCK for a while and have already gotten some interesting observations from the program. My lab works with platinum drugs such as cisplatin and oxaliplatin and we are looking for possible disruptions in protein-RNA interactions when bound to platinum.
I have created pdb files of single strand RNA bound to oxaliplatin. When using these structures, if the platinum is not part of the surface interaction, the platinum stays in place. When I attempt to have the platinum be part of the surface interaction it appears to be acting as an ion (which makes sense given the support for platinum ions) and is excluded from the surface interaction and is moved away from both biomolecules. Is there a way to get around this so that the platinum “ion” is held in place relative to the RNA? Alternatively, is there a different way to define the platinum molecule so that it is not read as an ion but a covalently attached molecule (or just some way to preserve the coordinate bonds to the platinum that are currently being broken between the RNA N7)?
Despite this program not being designed for what we work with, it has given us fascinating insight into the protein-RNA interactions and I look forward to continue working with it. Thanks!