ı have my thesis about multiple ligands -receptors interacting so how can I merge 2 ligand into one to docking simulation.I used PyRx software,UCSF Chimera software and autodock software and result is one by one not combination results .Can some body help me if you understand what I am saying.
If I understood correctly, you need to open all the protein-ligand docked complexes simultaneously in chimera and match the protein molecules. This can show you multiple ligand with protein.
And, if you want to dock more than 1 ligand with protein, then (1) it is rare (2) and I think you misunderstood something. Normally, multiple ligands are docked one-by one and then compare them to see their docking score, docked position, atoms involved etc. to evaluate their preferential binding pose and intensity.
You can prepare all the files, and run the loop to perform the molecular docking... Like the script below.
#!/bin/bash
for arqDpf in ./*_flex.dpf; do
arqDpfRen=`echo $arqDpf | cut -d'/' -f2 | cut -d'.' -f1`
../../bin/autodock4 -p ${arqDpfRen}.dpf -l ${arqDpfRen}.dlg
done
If you use PyRx you can add all the ligands you have before docking. PyRx does give you the liberty to do that with ease and have your binding score for all the ligands in a tabular form.
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