Using some crazy methods I've found a couple hundred regions of interest on sequence segments of multiple proteins and I'm looking to annotate them on 3D structures where available. However, since I'm dealing with mostly viral proteins many of the crystal structures are incomplete. Also, the sequences may differ slightly (with possible insertions or deletions) between my reference sequences and the crystal structure.
Also, most of the 3D structures have numerous side-chains. So in some instances a ROI which appears only once should actually be labeled multiple times in the crystal structure.
Does anyone know of a tool which can handle all of these instances in an automated fashion? I have plenty of programming knowledge so something that's scriptable would be fine. I just don't deal with crystal structures that often so I'm not familiar with the idiosyncrasies and the common toolsets out there.