Dear Dr. Elaine, Thanks for your detailed reply. It's helpful. Best regards, Ahmed On Monday, December 9, 2024 at 02:44:50 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmed, if you're asking whether ChimeraX predicts ligand-receptor binding modes, sorry, no it does not. If you are asking whether you can use the protein models from other modeling tools/programs to which ChimeraX has interfaces (Modeller, ESMFold, AlphaFold) for ligand-receptor docking, that is not anything that can be answered easily. It depends on how much information was put into the modeling, how much is already known, etc., and how exactly you intend to interpret the results. The bottom line is that you will have to rely on your own scientific judgement, including reading any published papers that have evaluated this issue. These programs also provide their own "model scores" and some of them even have a per-residue pLDDT reliability score. See the help for each related tool/command in ChimeraX (and of course, you can do your own literature searches on these methods outside of ChimeraX): <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 7, 2024, at 4:06 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:
Dear Dr. Elaine,
Greetings,
I would like to ask if it is possible to use ChimeraX-predictable models for docking with small molecules. Are there precautions for that?
Best regards, Ahmed