I already know a few programs/web severs; however, I'm looking to see if there's one in particular that's considered the "best" (i.e. most preferred) in terms of analyzing protein-ligand interactions. I've noticed that when analyzing different protein-ligand complexes on several of these programs/web servers (e.g. UCSF Chimera, Discovery Studio, Protein-Ligand Interaction Profiler, etc), I sometimes get different results; therefore, any guidance or assistance with this would be really appreciated. Thank you!
Mr. Schuster,
ChemBio3D:
[https://www.cambridgesoft.com/Ensemble_for_Chemistry/details/Default.aspx?fid=13&pid=668].
Different programs, different definitions of interactions. A suitable program is such that allows the user to (re)define and visualize and write to file protein-ligand interactions.
You can also try LigPlot. However, it needs institutional email address.
https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
Check https://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0118-5
Also check https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3352-x
Discovery Studio Visualizer Software (BIOVIA, Dassault Systemes) all the way.
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