Dear all,
Currently i am running docking studies using AutodockTools 4.2. For the protein optimization stage, why do we need to add hydrogen atoms as well as charges into the protein? What is the reason behind?
Your answer is highly appreciated!
Thanks in advance.
What Filip says is ok. In addition, the definition of at least the polar hydrogens allows the establishment of hydrogen bonds that may be present between the macromolecule and the compounds tested. The docking algorithms contemplate these forces of intermolecular union, and their non-definition, would not allow to contemplate them when calculating the binding energy of the compounds to the target, making a mistake by omission.
To expand on the above reply: not only does the pdb file not have hydrogen atoms, but the docking software requires the hydrogen atoms to be in place. Same with the charges: charges are not recorded in a crystal structure file, but many algorithms will want some sort of charge in place to run calculations with.
In addition to above answers, we virtually try to create and observe in-vivo condition for protein-ligand or protein-protein complex in molecular docking simulation. Macromolecules present in charged form with no atom missing in human/animal body. So, it is necessary and sensible to add charges and missing atoms (hydrogen and in some cases non-hydrogen) to protein before proceeding for docking experiment, irrespective of docking tool/software and algorithm you use.
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