How can I dock more than one protein with more than one ligand, I know that pyrx is the software which docks 1 protein with multiple ligand but how can I do it for multiple proteins with multiple ligands?
If you have a basic level in python, you can create a list for receptors files and another list for ligands. Then write a for loop to iterate over the receptors and ligands.
Hey Jameel M. Abduljalil I have done as you said now I come across another majar problem which is of parameters for docking this parameter are not always same for each protein how can I set different parameters and how do I know which parameter to use for that perticular protein is there any way to find out this parameters ?(I know who to find it manuallly using autodock tools but I dont know how to code for it)
(I have attached me code here)
Is not it less painful to work with a single pritein every docking run?
What parameters do you mean?
Are these receptors for structurally similar proteins or conformers of a single protein?
If that's the case, then just superimpose all the receptors and save it as multimodel pdb file. Then use this pdb file to generate pdbqt files. By this trick, you can use the same configuration file for all receptors.
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