Hi all,
I am trying docking protein-protein interaction. Is it necessary that i should remove heteroatoms from the protein structure, since its making main bonds between the amino acids?pls let me know.
Its ending up with the results like non-resideus ACE, clean the structure and apply charmpolar force.
It depends, if those het atoms are necessary for your proteins to interact, then nope, otherwise remove them. If these het atoms are part of crystallization process, you should remove them.
You need to prepare your system as well, make sure all atoms are present, geometry is optimized and protein is minimized. Pay attention to missing parts and secondary structure mismatch, just in case.
Once your proteins are ready, then go for docking.
Last point, avoid blind docking, search literature and see if binding residues are reported (if not for this protein, may be for homologous protein), and used them as starting point.
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