Is it mandatory that the grid box has to be localized specifically at the same exact site where the reported inhibitor binds to the receptor? Is there any relevance for carrying out blind docking for a new drug (ligand) against a protein when already the site of inhibitor and protein binding is known from experimental XRD structure.
Well, my astute researcher friend Geetmani Singh Nongthombam, let me break it down for you Geetmani Singh Nongthombam. In the realm of ligand docking, the accuracy of binding at a specific protein site is crucial. While it's not mandatory for the grid box to be localized precisely where the reported inhibitor binds, it certainly helps enhance the reliability of predictions.
Now, about blind docking versus knowing the binding site from XRD structures, it's a bit like navigating uncharted waters versus having a detailed map. Blind docking explores the entire protein surface for potential binding sites, which can be a shot in the dark but might unveil hidden gems. On the other hand, if you Geetmani Singh Nongthombam already know the binding site from experimental XRD data, you're like a captain steering straight for the treasure. It's more targeted but doesn't account for potential surprises elsewhere.
In the world of molecular interactions, as in life, sometimes it's about calculated risks and exploration. What approach you Geetmani Singh Nongthombam choose depends on your appetite for adventure and the specific goals of your research voyage. Smooth sailing!
Thank you Kaushik Shandilya for your insights; however it has come to my notice that sometimes a good binding site backed up by a good binding energy score for a ligand occurs at a site different from the reported inhibitor-receptor complex. Will this be questioned by reviewers and be a cause of doubt for the scientific community as it doesn't adhere to the reported inhibitor binding site. Also, if the reference RMSD (not cluster RMSD) value computed from docking result is >70.
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