Looking at docked data with the receptor shows as surface
To whom it may concern, Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes. My inquiry is this: Does AutodockVina take into account surface projections when performing docking? Thank you so much for your time, Jonathan Wang
Hi Jonathan, Autodock Vina and the Autodock prep scripts it calls were developed by a different group, and Chimera just communicates with a web service to run the docking part. Thus I’m not an authority on the program, and for details you should probably consult the Autodock Vina website, publication, or its developers: <http://vina.scripps.edu/> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641/> Nevertheless, here are some thoughts as to how it works and what you should check. As I understand it, AutoDock Vina does not use the surface per se, but it takes into account the (nonhydrogen) receptor atoms, and should not give a good score when ligand atoms are too close to receptor atoms. One thought is that maybe although the structure you are viewing is a trimer, what was returned by the receptor-prep script and actually used in the docking calculation was some smaller set of atoms, such as only the monomer. If you entered “/location/name” as the output file in the Chimera dialog, then this prepared receptor file would be /location/name.receptor.pdbqt. You should open this file in Chimera, and verify that it contains the receptor atoms you expected. (I do not know if this prep script handles multimers correctly.)
From the Chimera manual page <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> :
Output file - location and filename prefix for output files. If the prefix is name, the files generated by a successful run will be: • name (or name.pdbqt if indicated in the file browser) - docking results in PDBQT format... • name.receptor.pdb - receptor PDB file from Chimera, input to the AutoDock receptor preparation script • name.receptor.pdbqt - processed receptor in PDBQT format, input to AutoDock Vina • name.ligand.pdb - ligand PDB file from Chimera, input to the AutoDock ligand preparation script • name.ligand.pdbqt - processed ligand in PDBQT format, input to AutoDock Vina • name.conf - AutoDock Vina configuration file Another thought is that the calculation failed to find any positions of the ligand and it is just in the original position as input to docking. However, this would probably be fairly obvious. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 20, 2017, at 12:30 AM, Jonathan Y Wang <wang.ying.jonathan@utexas.edu> wrote:
To whom it may concern,
Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes.
My inquiry is this: Does AutodockVina take into account surface projections when performing docking?
Thank you so much for your time, Jonathan Wang
Thank you so much for your help and your timely response! I appreciated how clear your explanations were and your thoughts on how each might've occurred. Have a blessed day, Jonathan Wang On Mar 20, 2017 12:52 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Jonathan, Autodock Vina and the Autodock prep scripts it calls were developed by a different group, and Chimera just communicates with a web service to run the docking part. Thus I’m not an authority on the program, and for details you should probably consult the Autodock Vina website, publication, or its developers: <http://vina.scripps.edu/> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641/>
Nevertheless, here are some thoughts as to how it works and what you should check.
As I understand it, AutoDock Vina does not use the surface per se, but it takes into account the (nonhydrogen) receptor atoms, and should not give a good score when ligand atoms are too close to receptor atoms.
One thought is that maybe although the structure you are viewing is a trimer, what was returned by the receptor-prep script and actually used in the docking calculation was some smaller set of atoms, such as only the monomer. If you entered “/location/name” as the output file in the Chimera dialog, then this prepared receptor file would be /location/name.receptor.pdbqt. You should open this file in Chimera, and verify that it contains the receptor atoms you expected. (I do not know if this prep script handles multimers correctly.)
From the Chimera manual page <http://www.rbvi.ucsf.edu/chimera/docs/ ContributedSoftware/vina/vina.html> :
Output file - location and filename prefix for output files. If the prefix is name, the files generated by a successful run will be: • name (or name.pdbqt if indicated in the file browser) - docking results in PDBQT format... • name.receptor.pdb - receptor PDB file from Chimera, input to the AutoDock receptor preparation script • name.receptor.pdbqt - processed receptor in PDBQT format, input to AutoDock Vina • name.ligand.pdb - ligand PDB file from Chimera, input to the AutoDock ligand preparation script • name.ligand.pdbqt - processed ligand in PDBQT format, input to AutoDock Vina • name.conf - AutoDock Vina configuration file
Another thought is that the calculation failed to find any positions of the ligand and it is just in the original position as input to docking. However, this would probably be fairly obvious.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 20, 2017, at 12:30 AM, Jonathan Y Wang < wang.ying.jonathan@utexas.edu> wrote:
To whom it may concern,
Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes.
My inquiry is this: Does AutodockVina take into account surface projections when performing docking?
Thank you so much for your time, Jonathan Wang
On Mar 20, 2017, at 10:52 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
One thought is that maybe although the structure you are viewing is a trimer, what was returned by the receptor-prep script and actually used in the docking calculation was some smaller set of atoms, such as only the monomer. If you entered “/location/name” as the output file in the Chimera dialog, then this prepared receptor file would be /location/name.receptor.pdbqt. You should open this file in Chimera, and verify that it contains the receptor atoms you expected. (I do not know if this prep script handles multimers correctly.)
P.S. It may also depend on how you generated the trimer. In the Chimera dialog for AutoDock Vina, you have to specify a single model as the receptor. If you made the trimer from the monomer using the “sym” command, for example, it could be more than one model, so you would have to combine them first. This could be done with the “combine” command or with the “copy/combine” function in the Model Panel. However, this is not relevant if your trimer was already a single model. Elaine
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Jonathan Y Wang