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Specialty Chemistry Forums => Biochemistry and Chemical Biology Forum => Topic started by: ayush0963 on January 30, 2025, 04:51:21 AM

Title: Optimizing a ligand through docking
Post by: ayush0963 on January 30, 2025, 04:51:21 AM

We are doing some covalent docking studies.  Now that we have the results, how do we go about improving our compounds to bind more strongly?  Is it done intuitively or is there a systematic way to work?  I am a docking neophyte.

Title: Re: Optimizing a ligand through docking
Post by: Babcock_Hall on January 30, 2025, 10:32:21 AM

I empathize, having been in this situation (there is probably an old thread somewhere).  I am not aware of a systematic way, but I would appreciate hearing about one.  Which program are you using, and does it allow the side chains to have some freedom?