I have a protein structure that is in the Protein Data Bank (PDB) and I am trying to predict ligands that may bind to it. This is for the purpose of inhibiting the protein by blocking a certain binding site that I know with a small ligand or inorganic molecule. I wanted to have some possible leads before any actual assays are done in the lab. I have searched through many papers and google results for webservers or programs/pipelines that will predict ligands that may possibly bind to this protein. However, every server that I find is mostly predicting the binding sites that ligands may bind to. I already have a binding site on the protein that I'm interested in and actually only need to predict the ligand that may bind to that site.
For example, this webserver https://probis.nih.gov/ and a few others do what I want for the most part. However, they only return large proteins for the "ligand" that may bind to my target. I'm looking for smaller proteins that are probably somewhere in the neighborhood of 30 amino acid residues or less. Also, small inorganic molecules are acceptable as well.
Is anyone familiar with any standard way to do this kind of work? My only other ideas involve just typing a random string of residues into a structure prediction program and using one of the webservers that verifies protein-ligand interactions. However, I feel like there must be a software or server that automates this or does a more optimal search.
--In short-- I would love to find a webserver or program (able to be installed on a linux server) that will find small ligands or inorganic molecules that may bind to my target in the PDB and then let me pick a binding site that I already know to assess how good the predicted ligand interactions would be at that binding site.
