Hello all,
I have some problems with docking, Details are listed below. Thanks in advance!
links: PTN11(https://alphafold.ebi.ac.uk/entry/P35235); Respiratory complex I(https://www.rcsb.org/structure/6ZTQ); Respiratory complex III(https://www.rcsb.org/structure/7O3H)
Aim: Explore the interaction of PTN11 and Respiratory complex I(NDUB8 subunit) and PTN11 and Respiratory complex III(QCR2 subunit)
Questions:
1.PTN11 in the cytoplasm, but the other two proteins are inside the membrane. How do I determine the possible site of interaction between the two proteins?(Need to find the extracellular region of Respiratory complex I or III?)
2.For PTN11 structure predicted by alphafold, Whether it can be used for docking?
3.My aim is to explore the interaction of Respiratory complex I or III subunits(NDUB8 or QCR2) with PTN11.I don't know if I can just extract the corresponding subunits and remove the other components.
4.I am new to protein docking, When preprocessing proteins, I don't know the difference between add al1 hydrogens and add polar hydrogens. Meanwhile, in the protein subunit, i find have some amino acid gaps. Do I need to make up these gaps so as not to affect the subsequent docking?
