How to install and use Ligplot plus for receptor ligand interactions (Simple tutorial)
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- Опубліковано 15 вер 2024
- #ligplot+ #protein #structure #biology #PyMol #comsats #english #hindi #urdu
1- Steps for installation of Ligplot+
2- Libraries required for LigPlus installation are JDK/JRE.
3- Go to the Java website and download www.java.com/e....
4- Now go to the ligplot website www.ebi.ac.uk/....
5- You need to fill a form to get a license for downloading ligplus.
6- For that, you will need an institutional email address.
7- After downloading, extract the ligplus folder in your C:/program file.
8- Open a Ligplus folder and choose openwith with JRE Platform.
9- You need to define the paths when you're running ligplot+ for first time C:\Users\***\***\LigPlus.
10- After performing docking, PyMOL and Ligplot+ softwares are used to analyze the Protein-ligand structures.
11- Open the PyMol software as we have seen in our last tutorial, how to generate the structure using PDB File.
12- Open the PDB File of the protein,select the best model now go to actions, select reset - ligand sites - cartoon.
13- You can see the 3D Receptor-ligand Model.
14- Now to analyze the Ligand receptor interactions go to the ligplot+ software.
15- You need to import the Ligand molecule that you have generated using Pymol software.
16- Open the pdb file of Receptor ligand molecule in ligplot+ and select run.
17- Here you can see the hydrogen bond interactions between amino acids and ligand.
18- Analyzing the neighbouring residues and Interacting residues.
19- You can also customize your search by resizing ,changing colours and adding labels, Atoms and bonds.
20- Now your Ligplot image is ready to export, you can see it in PDF Reader or XPS Viewer.
21- Bye.
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Dear Dr. Farhan,
Thank you for your educative tutorials.
Thank you dr. Farhan for this tutorial, now, i can open ligplot ❤🙏
Pleasure
OMG it was so helpful.I really don't know that for running ligplot, java is needed.Last 1week i was searching this type of video.Thak you so much.Now it's done. 😍
Glad to know
Explained beautifully in a simple and comprehended way.
Finally I could be able to install ligplus on my comp without any pain thanks to you !
Really helpful. Thanks a lot brother
You are most welcome
really helpful..thanks doc..
Welcome sir
Sir finally winRAR helped Alhamdulillah, now it is running smoothly...
baraka allaho fik dear brother
I have java latest version and i downloaded ligplus also but it is not installing can you please help me
Thank you so much, because your education i can instal ligplot. Before i see your video i cant install this apk 🍭💜
Pleasure
Very good, Thanks
Thanks
thank you so much, sir
Hi Farhan! Thank you so much for this tutorial. Would you like to guess the issue when I extract the downloaded folder, I don’t see the LigPus Jar file, though it works fine on my other system. At first I thought the Java might not be installed correctly so I repeated, restarted the computer, but the problem is still there. I only see the cLigplus (.bat file) and Lib folder but I can see the Ligplus jar file. It’s so strange.
Thanks I succeeded to install ligplot.
Good to know
Thank you so much, Farhan!
many thanks. helped a lot
Thank you so much for this video!!!
Pleasure
I can't able to install LigPlus. It shows "Parameter file not found", How to rectify this prpblem?
very useful. thank u
jazakAllah
I cannot run ligplot after conversion, for some reason java isn't working even when I try to open the application it isn't
please check your java version, if its compatible with your Operating System and reinstall ligplot.
Same problem here. Did you have solved yours?
Sir I checked my PDB file ,it has ligand structure correctly inbuilt in the protein structure using pymol or chimera but when i run ligplot it is again showing the same, don't know where I'm going wrong ...sir plz help or if somehow I can send u dat PDB file u can check it by urself...
Thank u 👌🙏
Hi sir! I am getting the following error while installing ligplot. can you help me?
"Unable to recognize your operating system: Windowa 11
The graphics viewer will still work, but the LIGPLOT executables will not.
To Solve: see Common problems in installation Insruction."
I am receiving the same problem, did you find any solution? By the way your user name seems to be Turkish so if you are you can directly answer in Turkish
does the mail approval takes a long time ?
Sir when I am running ligplus,the ligplot doesn't display ligand structure as whole rather a part of it appears and so r the amino acid residues ,how to fix it??
No . Recheck your downloaded pdb file again.
i have not institutional email id, can u get by others way (
how one can increase the size of distance i.e 3.5 etc.. i wanna increase its size but could not find an option for it.
Go to the option size selection/ size definition.
It will allows you to change the size of each object in your plot.
Actually I followed all the steps carefully n it is getting downloaded as ligplus.zip but when it comes to check it in folder it doesn't appear as ligplus.zip but something as getfile.pl...can it b due to I don't hv any software installed in my PC which could extract files from this zip file like winRAR or any other??
I dont think that is the problem. However, you can try this as well. Problem is with downloading or may be the with the target folder.
Aaaaaa finally....Thank you so much🥰
Welcome
Assalam-u-alaikum bro ,can u plz help me to fix a problem which I'm goung through while downloading ligplot n java...actually whenever I download ligplus ,it is displayed as getfile.pl not as ligplus.zip in download section of my PC, plzzzz reply soon...
It is very strange. Just follow the steps showed in first two minutes. You just have to register on the website. It will send you email and password. Just use that username password and download ligplot plus 0:00 to 2:00
Or the file.may be downloaded somewhere else. Check your download section more carefully
If we want to find interaction between protein and and other ligand that is not a part of protein, will we use ligand output 1 or ligand itself in ligplot?
Hello Zainab
First you need to generate the model (protein+ other ligand) in Pymol only then you can analyze the interactions accurately using ligplot.
@@FarhanHaqj sir If the protein has already ligands attached to it, then should we have to remove them to find the interaction of that protein with other ligands?
No. protein can have binding sites for more than one ligand.
They are located in different parts of the protein, So we can study the interactions with different ligands attached.
@@FarhanHaqj got it sir... But why 2D structure of protein ligand interaction shown in Discover studio Visualizer is different from 2D structure in Ligplot?
Because all these softwares works on different algorithms. For specifically 2D protein ligand interactions MOE, Ligplot, Glide and Discovery Studio can be used. Plus Ligplot shows more valid and reliable results
Give me software pls
Àa
Thanks