I am docking three ligands with more than one proteins. Two of the ligands are already approved drugs and third is a plant compound. My all ligands accepts gasteiger charges and docking went smooth. I have also performed docking by adding kollman charges but my two approved drugs were not getting charges as the pdbqt file was not getting saved by adding gasteiger charges but i was able to get pdbqt file of plant compound successfully and interestingly I have got more negative binding energy values for plant compound by adding kollman charges than gasteiger charges. Is it normal to add kollman charges to ligands? can i report it? And as I have to compare all the ligands. Can I add in my paper the values of plant compund with kollman charges?
That saving issue should not occur. Please verify the steps
For standard docking all the ligands should be allotted same charges.
Nishat Malik,
Kollman and Gasteiger charges need to be fitted appropriately based on the nature of the ligand- either it is synthetic or a plant compound. As you had mentioned, your study contain both synthetic as well as plant compound, standard docking can be performed for all the compounds with same charges, further, residues has to be checked properly. This step is for preliminary standardization. Based on the obtained binding energy values, cluster and reference RMSD values (Root Mean Square Difference) and Ki values (Inhibition constant), further alteration of Kollman and Gasteiger charges can be carried out and further docking should be performed. Maximum negative values are an indication of maximum binding affinity of the ligand molecule. If your plant compound possess higher negative value, it indicates that your plant ligand has more ability to inhibit the corresponding target protein molecule.
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