I have a 3D-structure of a protein, but it is an apoprotein. I am using Maestro for molecular docking. I want to find out the protein binding site in my protein.
Maestro is the visualizer and GUI of the Schrodinger Suite, it does not perform molecular docking. You must be using the Glide module of Schrodinger Suite for docking.
In order to identify the binding site, you can use the Schrodinger module called SiteMap. It will identify all the probable cavities in the protein. If you want to use open source tools then there is a tool known as Castp that also does the same thing.
Thank you for the answer. I have another question. If we have a dataset of ligands which do not have any potential biological history with our target protein as the dataset has been downloaded from ZINC15 database. And we want to develop an e-pharmacophore model from this dataset. Can you tell me how can we do this?
You can use the HADDOCK
https://wenmr.science.uu.nl/haddock2.4/
You can use the CLUSPRO
https://cluspro.bu.edu/login.php?redir=/queue.php
Go to task and search for sitemap. Make sure your protein is on the workplapace.rename it and click on run.
After identifying the sitemaps, go to task again and select receptor grid generation.
Under receptor, select entries.
Under site, select centroid of workspace.......
Rename the go back to your workspace. Pin down the protein and the fisrt sitemap.
I have a similar question here. After generating the binding sites using sitemap and lets say l get 5 binding sites. From these 5 binding sites how do l know which one is the best site and select that one?!
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