I have attached an image and want to know what does the colour of spheres indicate ( for example the red sphere) and what probable things should I be searching while analyzing my results. Explain in detail all parameters to consider in the search (I mean visual search in the 3D space of the docked conformation)
I Thinlk for clear analysis of result you should try Ligplot as it will give you a good representation of no. of hydrogen bonds formed between the ligands and protein.
Mayank Agarwal..pls suggets me how can i download. i was having having problem installing as a .jar file is provided which i practically dont know to download..explain pls
The colored spheres are the van der waals radii for the respective atom. the color depicts the charge. You will able to generate a color key using the software... I think red is for negative and blue is for positive charges, but pls check this carefully.
firstly you have to download the ligplot from its website using academic mail.After downloading the zip file you have to extract it which will give you 3 files,out of which you haave to use LigPlus(i.e Executable jar file).you cannot install the logplot on pc as it dont have any .exe file
Then browse for the pbd file having the cordinates of protein and ligand both and analyse the result.
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