Hi, i am now doing my research for docking of tubulin to taxol and vinblastin using HADDOCK Webserver. I extract the ligand from bound crystal PDB file. Then, i supply the active residue using the hydrogen and hydrophobic interaction residue stated in PDBsum (1z2b and 1jff). After i get my docking result, i plot the interaction of protein-ligand complex using ligplot and compare with original PDB file.
So, first, my question is that how should i explain to my panel if my docked results are not same as with the original PDB file. Second question, is there any way to improvement the result of docking using HADDOCK.
Would appreciate if anyone can kindly explain. Thank you