Hi, thanks for the video, i am doing docking between peptide of 25 residues and graphene sheet(4*4) but in site finder nothing shows up and at the end it says site contains no atoms. Can you help me to resolve this issue please?
Thanks for the wonderful video. I've done docking for a series of GPCR with their native ligands using MOE. Unfortunately, the obtained affinity and rmsd aee not reproducible. I did as below: First I downloaded a pdb file. Removed all unwanted compounds and water molecules. In presence of the native ligand I did a quickprep. Finally docking (by default parameters). Could you please help me with my problem? By the way I saw in some video, some people do minimization before quickprep. Do you suggest it?
That's a difficult one and I have also have synthesized compounds where the docking data did not match the actual binding data. The first thing I would try is to change the parameters. Try both induced fit and rigid receptor, and increase the number of poses to get the best possible results. Also make sure specific parts of the ligand are protonated or deprotonated to be correct under biological conditions. If you are still not getting the correct results, you could try creating a pharmacophore. If you are docking with the native ligands, it is likely known what H-bond interactions are formed and you may be able to create pharmacophores to induce these interactions to occur. One other thing to consider is you could try other programs in addition to MOE such as Shrodinger and Pymol because these programs have slightly different coding and often give you slightly different results. You can definitely do minimization before quickprep, but I don't think it would make much of a difference. Hopefully this helps, thanks.
@@saidmoshawih9959 It definitely could be a good idea to take the average as long as the best poses have the correct H-bond interactions and other interactions. For publication purposes though, often just the best/most accurate docking score is reported.
Thanks for the explanation. I just want to know if there is a ligand preparation module in MOE, so it will be easier for the user to get all possible protonation forms, isomers, and tautomers. Secondly, what if I have a list of smiles as a ligand database to be downloaded, how can we download it? Thanks
There is a sort of ligand prep module. It can be found if you have a database open, go to compute in the database, then molecule. Here you can find the wash function to ensure everything is protonated/deprotonated correctly as well as other functions to prepare the ligands. It is not perfect though because I have docked compounds with multiple rotamers before and I had to draw and dock each individual rotamer because MOE does not choose one over the other. As for the SMILES question, I have created a SMILES string before but have never used one in MOE, so unfortunately I will not be much help there. Thanks
Hello sir I am trying to dock the ligand in the active site but the site is not at all visible after giving apply and close and also the poses are visible but the docked ligand is not visible sir how can it be treated sir?
You have to choose for yourself which is the best confirmation based on the docking score, if the pose is correct, and if it is picking up the necessary interactions.
Hello. I am trying to do docking in MOE. I tried protonating 100 ligands in the same order, but the system said that the size of the vector was exceeded. Do you know how I can correct this? Or what is the maximum size of the matrix to protonate?
I believe the issue may be due to the protein being too large, however, I am unsure what the maximum protein size is or how to adjust it to make it work. Sorry I could not be more help.
Usually its universities and companies that have a license for it because it is really expensive. You might be able to find a trial version of it somewhere.
@OrganicMechanismsChannel What about these 2 videos from this Chanel ua-cam.com/video/5FJfjUdbwqs/v-deo.htmlsi=_WnaOzPvJpWEkun8 Any steps correct for 4wxx pdb code zinc metaloenzyme?
Hi, thanks for the video, i am doing docking between peptide of 25 residues and graphene sheet(4*4) but in site finder nothing shows up and at the end it says site contains no atoms. Can you help me to resolve this issue please?
Thanks for the wonderful video. I've done docking for a series of GPCR with their native ligands using MOE. Unfortunately, the obtained affinity and rmsd aee not reproducible. I did as below:
First I downloaded a pdb file. Removed all unwanted compounds and water molecules. In presence of the native ligand I did a quickprep. Finally docking (by default parameters).
Could you please help me with my problem?
By the way I saw in some video, some people do minimization before quickprep. Do you suggest it?
That's a difficult one and I have also have synthesized compounds where the docking data did not match the actual binding data. The first thing I would try is to change the parameters. Try both induced fit and rigid receptor, and increase the number of poses to get the best possible results. Also make sure specific parts of the ligand are protonated or deprotonated to be correct under biological conditions. If you are still not getting the correct results, you could try creating a pharmacophore. If you are docking with the native ligands, it is likely known what H-bond interactions are formed and you may be able to create pharmacophores to induce these interactions to occur. One other thing to consider is you could try other programs in addition to MOE such as Shrodinger and Pymol because these programs have slightly different coding and often give you slightly different results.
You can definitely do minimization before quickprep, but I don't think it would make much of a difference.
Hopefully this helps, thanks.
I think it is also good to take the average docking scores for the best poses that resemble the cocrystalized ligands. Correct me if not right 😅
@@saidmoshawih9959 It definitely could be a good idea to take the average as long as the best poses have the correct H-bond interactions and other interactions. For publication purposes though, often just the best/most accurate docking score is reported.
Thanks for the explanation. I just want to know if there is a ligand preparation module in MOE, so it will be easier for the user to get all possible protonation forms, isomers, and tautomers. Secondly, what if I have a list of smiles as a ligand database to be downloaded, how can we download it?
Thanks
There is a sort of ligand prep module. It can be found if you have a database open, go to compute in the database, then molecule. Here you can find the wash function to ensure everything is protonated/deprotonated correctly as well as other functions to prepare the ligands. It is not perfect though because I have docked compounds with multiple rotamers before and I had to draw and dock each individual rotamer because MOE does not choose one over the other. As for the SMILES question, I have created a SMILES string before but have never used one in MOE, so unfortunately I will not be much help there. Thanks
Hello sir
I am trying to dock the ligand in the active site but the site is not at all visible after giving apply and close and also the poses are visible but the docked ligand is not visible sir how can it be treated sir?
I also want to know if we have more than one binding pocket, how do we choose one of them?
Definitely, check out this video: ua-cam.com/video/1RUzD8ZA0RM/v-deo.html
Thank you so much.please how can download this program .please we need link to install it.thanks
Its a pretty expensive program that usually a university or company will get for their employees. Often times people use PyMOL as a free option.
In results table, how can i choose which is the best conformation of ligand for target protein?
You have to choose for yourself which is the best confirmation based on the docking score, if the pose is correct, and if it is picking up the necessary interactions.
Hello.
I am trying to do docking in MOE. I tried protonating 100 ligands in the same order, but the system said that the size of the vector was exceeded. Do you know how I can correct this? Or what is the maximum size of the matrix to protonate?
I believe the issue may be due to the protein being too large, however, I am unsure what the maximum protein size is or how to adjust it to make it work. Sorry I could not be more help.
Thank you.please how can get this softwear
Usually its universities and companies that have a license for it because it is really expensive. You might be able to find a trial version of it somewhere.
@@OrganicMechanismsChannel thank you. I tried to get a trial version but i could not
Please suggest me steps for prepare metalloenzyme 4wxx pdb code
Have you tried the steps in this video: ua-cam.com/video/zH8uucGP3Tk/v-deo.html
@OrganicMechanismsChannel
What about these 2 videos from this Chanel
ua-cam.com/video/5FJfjUdbwqs/v-deo.htmlsi=_WnaOzPvJpWEkun8
Any steps correct for 4wxx pdb code zinc metaloenzyme?
Can i get free moe program
I am not sure if there is a free trial version or not. Usually it is universities or companies who buy a license because of how expensive it is