if the link between the domains is not part of the interface then perhaps a good first approximation may be to "cut" the linker and then use a program such as APBS to compute the binding energy..
> Hi, > > Recently we determined two structures of the same protein in complex with > different molecules. The protein contains two domains (called domain A > and > B here). In the two structures, domain A and B have different > arrangements > relative to each other, resulting different interaction interface. I want > to know which inter-domain interaction is stronger. Is there a way to > quantatively compare the "interaction energy or intensity" between the two > domains? I have calculated the buried surface area. However, just > comparing the buried surface does not provide definitive answer, given > that > the interacting residues on the interface are also different. > > BTW, we were not able to purify individual domains, so we cannot measure > the > binding affinity by wet lab approaches (so far). > > Thank you in advance for your inputs. > > -- > Best regards, > > Joe >
