Fwd: Inquiries on UCFS Chimerax
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
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
Dear Dr. Meng, Thank you so much for the detailed response, that is very helpful. Have a nice day! Best regards,Ahmed ========================= Ahmed Morsy, Ph.D. Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul05029, Korea C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr Orcidid: 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 On Wednesday, May 8, 2024 at 03:31:21 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: 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
Dear Dr. Meng, I hope this message finds you well. I am writing to you as we are planning to utilize ChimeraX for structural analysis in our upcoming research projects. As we prepare to integrate ChimeraX into our workflow, we are particularly keen to ensure that our approach and the resulting figures are in line with scientific standards and will be well-received by the academic community. To this end, we would greatly appreciate if you could provide us with any references or examples of published research where ChimeraX has been used for similar purposes. Specifically, we are looking for insights into how figures generated using ChimeraX have been formatted and validated in peer-reviewed publications. We aim to adhere closely to best practices and ensure that our use of ChimeraX enhances the credibility and scientific rigor of our findings. Any guidance, examples, or recommendations you could share would be immensely helpful. Thank you for your time and support. We look forward to your response and any assistance you can provide. Best regards, Ahmed Morsy On Wednesday, May 8, 2024 at 03:31:21 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: 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
Dear Ahmed Morsy, (1) if your institution has a subscription to a service like Web of Science, you can easily look up some ChimeraX paper and then find all or nearly all of the papers that cite it. I think you can also do it with a free service like Google Scholar but I haven't tried it myself. (2) on our home page lefthand side there is a "featured citations" list, and under it a link "More citations..." to see a selected set, but certainly not as complete as method (1) above. Home page: <https://www.rbvi.ucsf.edu/chimerax/index.html> (3) It seems like the larger question is "how should I do molecular modeling and visualization?" and maybe even "how to do structure-based discovery and design?", but these are very large areas, probably covered by many textbooks, and beyond the scope of this mailing list to address. You get experience and confidence about this by reading many papers in your field, seeing what steps they contain, and judging for yourself the quality of the research. Probably you would also take into consideration the reputation of the journal and the paper authors. It may not even matter that much whether they use ChimeraX, as they may use other programs for similar purposes. ChimeraX is a tool, and a very valuable tool, but you still have to carefully design your research projects based on your own knowledge. We try to provide reasonable examples in tutorials of things you might want to do, or features in the tools like ViewDockX that allow things you might want to do. 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 11, 2024, at 7:17 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:
Dear Dr. Meng,
I hope this message finds you well. I am writing to you as we are planning to utilize ChimeraX for structural analysis in our upcoming research projects.
As we prepare to integrate ChimeraX into our workflow, we are particularly keen to ensure that our approach and the resulting figures are in line with scientific standards and will be well-received by the academic community. To this end, we would greatly appreciate if you could provide us with any references or examples of published research where ChimeraX has been used for similar purposes. Specifically, we are looking for insights into how figures generated using ChimeraX have been formatted and validated in peer-reviewed publications.
We aim to adhere closely to best practices and ensure that our use of ChimeraX enhances the credibility and scientific rigor of our findings. Any guidance, examples, or recommendations you could share would be immensely helpful.
Thank you for your time and support. We look forward to your response and any assistance you can provide.
Best regards,
Ahmed Morsy On Wednesday, May 8, 2024 at 03:31:21 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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
Hello Dr. Meng, I appreciate your detailed explanation, precious advice, and useful links. ChimeraX is a potential program with various applications with high convenience. We are trying out best to utilize it for our research and trying our best to prepare a robust research article with that. Again, thank you for time and help. Best regards, Ahmed Morsy On Mon, May 13, 2024 at 1:08 AM, Elaine Meng<meng@cgl.ucsf.edu> wrote: Dear Ahmed Morsy, (1) if your institution has a subscription to a service like Web of Science, you can easily look up some ChimeraX paper and then find all or nearly all of the papers that cite it. I think you can also do it with a free service like Google Scholar but I haven't tried it myself. (2) on our home page lefthand side there is a "featured citations" list, and under it a link "More citations..." to see a selected set, but certainly not as complete as method (1) above. Home page: <https://www.rbvi.ucsf.edu/chimerax/index.html> (3) It seems like the larger question is "how should I do molecular modeling and visualization?" and maybe even "how to do structure-based discovery and design?", but these are very large areas, probably covered by many textbooks, and beyond the scope of this mailing list to address. You get experience and confidence about this by reading many papers in your field, seeing what steps they contain, and judging for yourself the quality of the research. Probably you would also take into consideration the reputation of the journal and the paper authors. It may not even matter that much whether they use ChimeraX, as they may use other programs for similar purposes. ChimeraX is a tool, and a very valuable tool, but you still have to carefully design your research projects based on your own knowledge. We try to provide reasonable examples in tutorials of things you might want to do, or features in the tools like ViewDockX that allow things you might want to do. 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 11, 2024, at 7:17 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:
Dear Dr. Meng,
I hope this message finds you well. I am writing to you as we are planning to utilize ChimeraX for structural analysis in our upcoming research projects.
As we prepare to integrate ChimeraX into our workflow, we are particularly keen to ensure that our approach and the resulting figures are in line with scientific standards and will be well-received by the academic community. To this end, we would greatly appreciate if you could provide us with any references or examples of published research where ChimeraX has been used for similar purposes. Specifically, we are looking for insights into how figures generated using ChimeraX have been formatted and validated in peer-reviewed publications.
We aim to adhere closely to best practices and ensure that our use of ChimeraX enhances the credibility and scientific rigor of our findings. Any guidance, examples, or recommendations you could share would be immensely helpful.
Thank you for your time and support. We look forward to your response and any assistance you can provide.
Best regards,
Ahmed Morsy On Wednesday, May 8, 2024 at 03:31:21 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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
participants (3)
-
ahmed morsy -
Elaine Meng -
Tom Goddard