After molecular docking simulation using autodock tools and saving the best hit as pdbqt file then converted it into pdb file using openbabel programe. The protein ligand interaction profiler online server cannot find any binding sites in the uploaded pdb file. I want to know what is the problem?
Thanks in advance.
In the file you sent me, there is no small molecule ligand. I therefore assume that you want to look at the protein-protein interface between the two chains in the structure. This interface corresponds to the dimer interface of your protein seen in the first hit I get for its sequence in the pdb.
The PLIP server has originally been designed to look at the interface between proteins and small molecule ligands, and only recently has been updated to also accept peptide ligands. Use the "Advanced Options" to set the analysis to the interaction between two protein chains. It seems to time out with your structure, which is not surprising with nearly 10'000 non-hydrogen atoms in either chain. You might have to use a tool more suited to protein-protein interfaces, such as PDBePISA ( https://www.ebi.ac.uk/pdbe/pisa/ ), or locally install PLIP or LigPlot+ https://www.ebi.ac.uk/thornton-srv/software/LigPlus/download2.html and use it in the "DimPlot" mode. However, due to the size and complexity of the interface, I would rather doubt that either PLIP or DimPlot could produce a reasonable image of all the interactions, therefore a listing of the interface residues from ePisa or similar is your best bet.
If you tried docking a small molecule ligand, you will have to check out where you lost your ligand - can you see it in the original pdbqt file? It is definitely not in the pdb file you sent me!
Analzying the .pdbqt file you sent me, I have come to the conclusion that neither the openbabel you used to convert it to a pdb file nor PLIP like the "END" record separating the receptor from the ligand. Everything after the "END" was ignored in either process. In contrast, PyMOL loads the atoms that come after the END statement into a separate object.
Hi,
First of all, you have to be sure that the ligand has properly docked into the protein binding site, then you have to create a complex between protein and docked ligand.
1. if you were using autodock vina, it proved 9 best conformations and you have to extract 1 best conformation, you can use python script provided in MGL-tools utilities directory and can use as:
python pdbqt_to_pdb.py -f docking_output.pdb -o X.pdb
2. further, you have to create complex with protein under study using following command:
cat protein.pdb X.pdb | grep -v '^END ' | grep -v '^END$' > complex.pdb
3. Now you can submit your complex.pdb file to the PLIP server and it will provide you with the desired results.
Cheers..!!!
- Badges
- Science topic
- Similar topics
- Filing