I tried to analyze the interactions in discovery studio between ligand (chemical compound) and receptor (protein) after docking in pyrx. But when I opend the docked complex in the discovery studio it showed only the receptor and failed to visualize the chemical interaction. What was the flaws in my process? How can I solve this problem? Any suggestion from you will be highly appreciated. Thank you.
Did you select (mark) the ligand compound? This could be done in the left side panel. Or separate the ligand from the complex and upload each one by separate in the same window
Hi Saruar Alam
I guess you have used Vina of Pyrx to dock. The outputs are stored in different folders, you need to make it as complex (protein.pdb+ligand pose.pdb) first. You can do this with simple PyMOL. After that make visualization with DS.
You can download the protein. Pdb and ligand. pose. Pdb separately and manually add the ligand to the protein to make protein.pdb+ligand pose.pdb
I am facing the same issue. The outcome of docking in Pyrx ia giving two separate files for protein and ligand in pdbqt format. But in DS I guess we require one single file. How to merge the two files?
Thanks, everyone. The problem has been solved using Pyrx to merge these two files.
I have done my docking using Pyrx, am I suppose to analyze@ all the nine conformations of a ligand using discovery studio or the conformation with the highest negative binding affinity?
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