Hi everyone, now i am doing my research about molecular docking protein-peptide using HADDOCK 2.4. when i analyze the interactions using ligplot, there are interactions between peptide and amino acid residue of receptor outside the binding site (active site). what that's mean? is it good or bad ? can anyone explain me. thank you..
Interactions between a peptide and receptor residues outside the active site can be beneficial and detrimental.
Beneficial in a way that it can enhance binding affinity. It can also stabilize the protein structure. Thirdly, this interaction can play a major role in allosteric interaction.
If we talk about its bad effects they are like unwanted interactions , structural instability, inhibition of function and sometimes it can reduce binding affinity as well.
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