Step by step docking
In this article, I am only going to SUPPLEMENT the tutorial provided at the DOCK website. Mainly the things which I found troublesome for me. So you should check out the tutorial first for a better understanding on the steps.
The steps in docking using DOCK are:
1) Structure preparation (enzyme and substrate)
For structure preparation, we will have to modify the 3D protein pdb file we have. I used a modeling program called Chimera (as what the tutorial advised), which is available free of charge from the Chimera website (http://www.cgl.ucsf.edu/chimera/). Structure preparation was a straight forward process. I mean, you only have to follow the tutorial to do so (it's already quite clear).
Just remember to prepare the charged mol2 structure of the ligand bound to the pdb protein's active site. You will need it if you want to be more efficient in the grid and sphere generating process. Even though you are not going to dock the ligand. I didn't identify this from the beginning, which created a problem in the sphgen - sphere generating procedure (it took too long, it could take for about 8 hours on my 1.6 Ghz centrino laptop with 512 RAM).
I did the structure preparations on windows, since I wasn't successful in installing the Chimera program on openSuse 10.2. Still remains a mystery for me up to now.
When you're finished with the preparation, now we can continue to the next step.
2) Sphere generation and selection
For generating the molecular surface of the protein, you will need a program called dms (as I have mentioned in my previous post). Installation was quite simple. Just type “make install” in the dms directory and stop there. You should have dms installed on your system (that's what happened to me in openSuse anyway). Remember that this is installation for a local machine. For parallel machines, there are other things you need to modify (check the dms readme that comes with the package).
When finished generating the molecular surface, use the program sphgen to generate the spheres.
Tip 1: copy the programs you want to use in your working directory!!.
Tip 2: in openSuse, instead of just typing “sphgen (options)”, I had to type “./sphgen (options)” to get it done!
After finished generating the spheres, now it's time to select the spheres you want to use as the active site. You can use the largest cluster created by sphgen, use a sphere in a selected radius, or select the spheres manually. I would recommend the second choice (use a sphere in a selected radius). Here, you should use the mol2 structure of the ligand bound to the pdb protein's active site (mentioned in step 1). This will save you precious time, believe me!
3) Grid generation
For this part, I had no problems at all. I just followed the tutorial, and I was home free.
4)Docking
There are 2 main ways of docking. First is the flexible ligand docking, and second is the rigid ligand docking. The flexible docking lets dock change the ligand conformation in response to the binding site. The rigid ligand doesn't let dock change ligand conformation. You should choose the one which suits your need.
For the docking process, thankfully I had no problems (I used flexible ligand docking). However, you might want to check the parameters that you need to tamper. For docking, I followed the dock v5.2.0 tutorial which is also available at the DOCK website.
Interpreting results
There are two main results that I found interesting (well, up to now, these are the only things I can analyze =)). First is the interaction energy of the ligand-protein complex. The lower the interaction energy, the stronger the bond is. I found this as additional data to supplement my kinetic experiments. Second is the conformation and orientation of the substrates in the binding site. Comparison with established ligand-protein structures can give better understanding on the effect of binding site structure has on substrate binding.
Well, this is a little taste of what DOCK can do for you. I have still much to learn about docking. But, since I am quite sure that it will be very important in future enzymatic studies, I have to spend more time to study it.
In this article, I am only going to SUPPLEMENT the tutorial provided at the DOCK website. Mainly the things which I found troublesome for me. So you should check out the tutorial first for a better understanding on the steps.
The steps in docking using DOCK are:
1) Structure preparation (enzyme and substrate)
For structure preparation, we will have to modify the 3D protein pdb file we have. I used a modeling program called Chimera (as what the tutorial advised), which is available free of charge from the Chimera website (http://www.cgl.ucsf.edu/chimera/). Structure preparation was a straight forward process. I mean, you only have to follow the tutorial to do so (it's already quite clear).
Just remember to prepare the charged mol2 structure of the ligand bound to the pdb protein's active site. You will need it if you want to be more efficient in the grid and sphere generating process. Even though you are not going to dock the ligand. I didn't identify this from the beginning, which created a problem in the sphgen - sphere generating procedure (it took too long, it could take for about 8 hours on my 1.6 Ghz centrino laptop with 512 RAM).
I did the structure preparations on windows, since I wasn't successful in installing the Chimera program on openSuse 10.2. Still remains a mystery for me up to now.
When you're finished with the preparation, now we can continue to the next step.
2) Sphere generation and selection
For generating the molecular surface of the protein, you will need a program called dms (as I have mentioned in my previous post). Installation was quite simple. Just type “make install” in the dms directory and stop there. You should have dms installed on your system (that's what happened to me in openSuse anyway). Remember that this is installation for a local machine. For parallel machines, there are other things you need to modify (check the dms readme that comes with the package).
When finished generating the molecular surface, use the program sphgen to generate the spheres.
Tip 1: copy the programs you want to use in your working directory!!.
Tip 2: in openSuse, instead of just typing “sphgen (options)”, I had to type “./sphgen (options)” to get it done!
After finished generating the spheres, now it's time to select the spheres you want to use as the active site. You can use the largest cluster created by sphgen, use a sphere in a selected radius, or select the spheres manually. I would recommend the second choice (use a sphere in a selected radius). Here, you should use the mol2 structure of the ligand bound to the pdb protein's active site (mentioned in step 1). This will save you precious time, believe me!
3) Grid generation
For this part, I had no problems at all. I just followed the tutorial, and I was home free.
4)Docking
There are 2 main ways of docking. First is the flexible ligand docking, and second is the rigid ligand docking. The flexible docking lets dock change the ligand conformation in response to the binding site. The rigid ligand doesn't let dock change ligand conformation. You should choose the one which suits your need.
For the docking process, thankfully I had no problems (I used flexible ligand docking). However, you might want to check the parameters that you need to tamper. For docking, I followed the dock v5.2.0 tutorial which is also available at the DOCK website.
Interpreting results
There are two main results that I found interesting (well, up to now, these are the only things I can analyze =)). First is the interaction energy of the ligand-protein complex. The lower the interaction energy, the stronger the bond is. I found this as additional data to supplement my kinetic experiments. Second is the conformation and orientation of the substrates in the binding site. Comparison with established ligand-protein structures can give better understanding on the effect of binding site structure has on substrate binding.
Well, this is a little taste of what DOCK can do for you. I have still much to learn about docking. But, since I am quite sure that it will be very important in future enzymatic studies, I have to spend more time to study it.
no yar..... for the past 2 weeks i am suufferin 2 kick start the docking procedure......
ReplyDeletedownloaded autodock 4.. but am not able to install properly.. in win-cygwin.....
:-( :( :(:(:(:(:(:(
I also tried using cygwin to no avail. I kind of forgot why I didn't continue to work on it though. Just remember to install the compilers you need before you install dock. In Opensuse or PClinuxOS, the procedures aren't that hard (I figured the compilers I need while installing).
ReplyDeleteHello ,Fendrri,I'm also a new student in dock.I tried dock with my receptor which has 385 residues.In first steps,it had no problem,but when running sphgen,there was an error.It generated more than 999999 spheres,but I don't know why it has so much.Is the receptor with 385 residues too big?
ReplyDeleteAny answer is appreciated!
@yolanda
ReplyDeleteSorry for the super late reply. I haven't been actively blogging lately. Let me tell you that I'm not an advanced DOCK user. I just used it according to the tutorial, and everything turned out OK. But let me share a little of my experience with you. My protein has approximately 380 amino acid residues, and the substrate binding pocket is actually really small. Perhaps under 30 residues are involved in the binding area. 385 residues is probably too much. If possible, try to pinpoint a specific area you want to test using the grid. You can also try to email prof. Irwin Kuntz (one of the founders of DOCK). He's a really nice guy. My email was replied promptly. I'm really sorry for not being too helpful.
Fendrri