Question: Is there any borderline of binding energy in docking stated that we should consider these ligands with its binding energy for further analysis?
1
gravatar for sakurashirleyke
22 months ago by
Malaysia
sakurashirleyke30 wrote:

Regard virtual screening. After docking, the results will show a list of ligands with their binding energy or binding affinity. A general statement usually stated that for "binding energy / binding affinity", the more negative the energy is, the better the ligand. For example, -9.0 binding energy, we can state that the ligand is better. But how we tell that "ligands with these lowest binding energy" should consider? or what is the "lowest binding energy" we should consider?

Now the question arise is, after docking, we usually will select the top ligands based on the lowest binding energy for further analyze or visualise in order to know more details about ligand. But regard the binding energy, is there any "border line" stated that we have to select the top ligands until what binding energy?. Meaning that, for example, we have the following result for about 20 ligands.

ligand binding energy ligand binding energy

1 -9.9                            11 -9.0

2 -9.9                            12 -8.8

3 -9.8                            13 -8.6

4 -9.7                            14 -8.2

5 -9.6                            15 -8.0

6 -9.5                            16 -7.5

7 -9.4                            17 -6.5

8 -9.3                            18 -5.2

9 -9.2                            19 -4.8

10 -9.1                           20 -4.0

Based on the result, we know that -9.9 is better, therefore we select ligand 1 and 2 for further analysis. But questions such as (following) will appear:
1) But we cannot state that we should not consider or select ligand 3 until ligand 11 for visualise...
2) we should not select ligand 12 and so on for analyse because the gap is different....
3) we said that -9.9 is better, but we can also said that -8.0 is better therefore, we should select the ligand from 1 until 14 for analysis...

If there is general border line of binding energy, we can tell that we should select ligand 1 till 11 because the border line statement state that we should select any ligand if their binding energy is above -9.0. If really got border line, we can select and visualise the ligand wisely, so that we will not miss any ligands that are potential to become inhibitor. Have this kind of "border line"? If have, can provide the article?

or how we should select the ligand after docking based on binding energy?

Thank you very much :)

ADD COMMENTlink modified 9 weeks ago by zappy0 • written 22 months ago by sakurashirleyke30
0
gravatar for zappy
9 weeks ago by
zappy0
zappy0 wrote:

I'm having the same question and for now, how I solve it is to find a ligand of reference. For example, let's say you are doing docking on a protein and the protein has a well-known inhibitor. A solution can be to add that inhibitor to your set of ligands. You then compare the binding energies of your ligands to the reference one.

ADD COMMENTlink written 9 weeks ago by zappy0
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