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Each edge in the network indicates either a binding interaction or a functional linkage or both between a pair of proteins.
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It should be possible to gain additional affinity by accessing an additional local binding interaction or filling a local hydrophobic pocket by using a structure-based design approach.
In this model, the protein can bind to its cognate element in a specific binding interaction, or it can bind in a distinct nonspecific binding mode, but not both simultaneously; i.e., the two binding modes compete with each other.
We note that the scaffold can contribute to bioactivity directly, via shape or binding interactions, or indirectly, via functionalization potential.
Considering the binding interaction, whether a given amino acid or nucleotide gives rise to a match or mismatch depends on the particular binding partner, so that the binding energy is a nonlinear function of the sequences at the TF and TFBS loci.
Identification of ligand-protein binding interactions is a critical step in drug discovery.
This process leads to the anchoring of the cells through specific binding interactions for a particular surface.
These conformations may be present prior to antigen binding as isomers (preexisting equilibrium mechanism), may appear during the binding interaction through rearrangement (induced fit mechanism), or a combination of the two scenarios may occur.
One such method is the structural interaction fingerprint [42], or molecular interaction fingerprint [43], which encodes into a binary bit string the set of binding interactions made by a docked ligand pose.
This experiment is useful because the previous techniques only imply a binding interaction.
Hsp90 is an ATPase, but the binding interaction with Unc45b is not affected by either ATP or ADP (data not shown).
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