Dear researchers
Need your expert suggestions please.
I am trying to get protonation states of my protein ligand by using pdb2pqr webserver version 2.1.1. However; when I get result propka file it does not give result for ligand atom and gives warning that Ligand atom have not been treated by propka 3.0.
What should I do with pdb2pqr for using propka 3.1?
I also tried
https://playmolecule.org/
for pka calculation but it only gives 1 pka value for ligand while I use propka 3.1 I get different ionizable sites for ligand.
I have 2 ligands in my protein how should I workout for protonation states correctly for both protein and ligands?
Thanks in advance.
Sadaf
https://s3-eu-west-1.amazonaws.com/.../D3R_Grand_Challenge_4__Ligand_Similarity...
Using schoedinger to determine the protonation state of ligand is the best choice I found up to now.
PROPKA works for protein but not for ligand. I suspect that the pKa of your ligand determined from PROPKA is wrong or you must mistakenly understand the output.
thank you all. Zhaoxi Sun I used propka 3.1 and it gave me ionizable group pka values for ligand. Could you please suggest if it is wrong?
thank you
propka3.1 does not support ligand calculation. You can check the official version yourself.
I think that you maybe use some derivatives provided by the software you use.
Zhaoxi Sun thank you for your suggestion could you please guide me by which suit I can calculate pka using Schrodinger. I downloaded Maestro with academic license but here I can not find pka calculation.
thank you in advance
Thank you SAMEE ULLAH
and Zhaoxi Sun for your valuable suggestions. I have used Marvin sketch for ligand pKa calculation. But my question is regarding pKa values of ligand when it is in the binding pocket surrounded by protein.As per my thinking (which may be wrong, please correct me if it is so) there should be a change in pKa values when ligand bind in the binding pocket depending upon the surrounding environment. So using pKa values for independent ligand (not bound to protein) is not a good approach as it would be different then the one bound in catalytic pocket.
I am not sure what propka3.1 then calculated regarding ligand atoms. I have attached .pka file for your review and suggestions please.
Thanks in advance.
Regards.
Sadaf
Hi Sadaf,
There is indeed a pKa shift When the ligand binds to the protein. However, modelling the free ligand is already challenging and cslculating the pKa shift makes it more difficult. I would say all existing methods are unable to provide an accurate estimate on hard/complex systems and thus considering the pKa shift of the ligand seems not very meaningful. So Just use the free ligand in your calculation.
- Badges
- Science topic
- Similar topics
- Filing