Dear Ahmed Morsy,
(1) Depends what you mean by "detecting" ... if you mean will it dock the ligand with the protein to predict where/how it binds, the answer is no.
If you mean you already have a structure of a ligand-protein complex (such as from experimentally determined structures or the output of some other protein-ligand docking program), then the answer is yes, you can use ChimeraX to analyze the interactions. For examples of what you could do, see the "protein-ligand binding sites" tutorial:
<
https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html>
See also the ViewDockX tool for looking at results output from other programs that do protein-ligand docking:
<
https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
(2) there is no standard. You have to use your own scientific (and for a paper figure, artistic) judgment, based on what you are trying to show and the details of the proteins you are interested in.
I hope this helps,
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 May 7, 2024, at 10:45 AM, Tom Goddard via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
>
> Please send ChimeraX questions to the mailing list unless they contain private data.
>
> Begin forwarded message:
>
> From: ahmed morsy
> Subject: Inquiries on UCFS Chimerax
> Date: May 7, 2024 at 4:52:22 AM PDT
> To: "goddard@cgl.ucsf.edu"
> Reply-To: ahmed morsy
>
> Dear Dr. Thomas Goddard,
>
> I hope this message finds you well.
> I am very thankful for your great tutorial on the UCFS Chimerax YouTube channel.
>
> I have a few questions that need your kind response:
>
> 1- Can we apply UCFS Chimerax for detecting the interaction between protein & ligand, or small molecule (from Pubchem library) and protein?
> 2- What is your standard for increasing or decreasing C-alpha distance (in Angestrom) to color the structure that is different between the Alphafold prediction and the experimental one?
>
>
> Thank you for reading my message, and I look forward to hearing from you.
>
> Best regards,
> Ahmed Morsy
> =========================
> Ahmed Morsy, Ph.D.
>
> Assistant Professor,
> Department of Stem Cell & Regenerative Biotechnology,
> Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
> Tel.: 02-450-0498
> C.P.: +82/10-5299-5844
> E-mail: ahmed_morsy86@yahoo.com;
ahmed@konkuk.ac.kr> Orcid id:
https://orcid.org/0000-0003-3873-9903 > Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400)
> Researchgate:
https://www.researchgate.net/profile/Ahmed-Abdal-Dayem > GoogleScholar:
https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en >