I am surprised with the zdock results for my peptide and 3 different receptors. I removed the polar hydrogens added Charmm forcefield and performed docking with zdock six degree of freedom and 54000 poses. Then reranked the poses with zrank -R after adding hydrogens. I know by experiments that my protein interact with only Receptor A, weakly with Receptor B and do not interact with Receptor C. However, in every cases I can find docking and the score are
myProtein-ReceptorA: -155.291; myProtein-ReceptorB: -144.119; myProtein-ReceptorC: -146.223
Could someone please tell me what is the Problem?
Hello Ashmit,
From my experience with ZDOCK, there is a strong possibility of getting a prediction that is not correct and from your results it seems that the highest bound protein is with receptor B with which the experimental results indicate otherwise. The docking depends on which orientatin the software has docked the protein into the receptor.
Sharing my experience, I think we have to put the experimental results and docking results together. In your results with receptor B, there should be one which is weakly bound than receptor A. and then see its pose and compare with the receptor A results.
You can also try using swarm dock server.
Hello,
as you told receptor C is not interacting but here in your result scores shows its interaction which is equal to receptor A..so ur result is wrong ..so i suggest u to try some other docking method
Hello,
as the comments from other researchers, I also think your docking result seems to have some problem. The results show that affinity is like receptor B>>A=C somehow. so far, why don't you restrict the interacting residues, which is considered as critical for ligand binding. Or you can use other software as well.
Sorry for the typo.. for receptor B it was myProtein-ReceptorB: -144.119; NOT 1449.119. I edited the post. I also tried autodock and there also results were not good. As per I know Zdock is one of the best Software for protein-protein docking.
With respect your result, the docking showed good result. More the negative more the affinitiy, so the docking of receptor-A and your protein is good.
Is, what you call a 'peptide' a flexible short amino acid sequence? In this case rigid body docking might not be the best option. I would suggest using flexpepdock instead http://flexpepdock.furmanlab.cs.huji.ac.il/
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