Hello Malathi,
The basic concept of docking is how the one molecule fits into another and interact with each other. The interactions might be of different types like hydrogen bond interaction, hydrophobic interaction, pi-pi stacking etc. So to know some of these interactions especially hydrogen bond network which ultimately helps to stabilize the ligand. as well as the protein itself. We need to add hydrogens.
In any protein, there is a specific site responsible for its activity so called active site which has specific shape and volume. The ligand has to fit into that active site cavity. If there is already one ligand present you cant put another one on top of it. This situation is similar to that of car parking, if there is no space in a parking lot and your wish is to park your car so simply you could not park your car on the top of existing car which already occupy the space. In the similar way we have to remove the ligand which is already present so as to make space for the new ligand in which you are interest.
Hello Malathi,
The basic concept of docking is how the one molecule fits into another and interact with each other. The interactions might be of different types like hydrogen bond interaction, hydrophobic interaction, pi-pi stacking etc. So to know some of these interactions especially hydrogen bond network which ultimately helps to stabilize the ligand. as well as the protein itself. We need to add hydrogens.
In any protein, there is a specific site responsible for its activity so called active site which has specific shape and volume. The ligand has to fit into that active site cavity. If there is already one ligand present you cant put another one on top of it. This situation is similar to that of car parking, if there is no space in a parking lot and your wish is to park your car so simply you could not park your car on the top of existing car which already occupy the space. In the similar way we have to remove the ligand which is already present so as to make space for the new ligand in which you are interest.
Absolutely its True.
"If there is already one ligand present you cant put another one on top of it. In the similar way we have to remove the ligand which is already present so as to make space for the new ligand in which you are interest. "
Dear Malathi,
Mr.Gaurao v. Dhoke said an answer with excellent example. he is correct. The addition of hydrogen helps to find the hydrogen bond interactions and more favorable to us to find binding affinity of ligand against protein.
A short mention deserve also water. All waters molecules (and ions) are normally removed as well before docking. In special case, key waters or "conserved" waters can be kept in the binding site, improving the results.
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