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For protein-protein interaction, Morihiro Hayashida et al. proposed novel methods using conditional random fields for predicting protein-protein interactions by utilizing the fact that mutual information between residues at interacting sites can be higher than that at non-interacting sites.
Studies aimed at identifying interacting sites between BBK32 and Fn revealed an interaction between the MSCRAMM and the Fn F3 modules.
The "independent sites" assumption is admittedly a convenient approximation, a simplification that is likely valid for a large majority of potential site interactions but invalid for a small fraction of interacting sites.
It is known that mutual information between residues at interacting sites can be higher than that at non-interacting sites.
These sensors contained single hydrogen-bond functional groups, which acted as interacting sites for fluoride ion.
Networks of interacting sites revealed that TPRs fall into two unrecognized families with distinct sets of interactions related to the identity of position 7 (Leu or Lys/Arg).
The strongly interacting sites disappear during the induction period and are proposed to be the sites where the isomerization reaction is initiated.
We have also analyzed the Tollip interacting sites of ARIP3 (Panels D and E).
As the freely varying sites mutate, however, interacting sites can switch between variable and invariant states.
Some HD links survive in evolution, but other links disappear because of mutations occurring at interacting sites in one or both of the duplicated proteins.
The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites.
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