Hi HyeYeon, I don't understand the question because ChimeraX does not predict protein-protein interactions.

Do you mean that you used the AlphaFold tool to run an AlphaFold multimer prediction? If so, probably the AlphaFold program has gone through some updates during that time interval that might change the results, and/or you used different settings to run the calculation.

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 Jan 22, 2024, at 3:16 AM, ‍정혜연[학생](생명과학대학 유전생명공학과) via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi, I'm HyeYeon from KyungHee University.

I am sending you an email because I have some questions while using ChimeraX.

When I investigated the interaction between the two proteins using chimeraX, the results of the two runs were different even though they had the same sequence.

One is the result from June of last year and the other is from January of this year.

Did the PPI results change despite the same sequence as a result of the program update?

I would appreciate it if you could check and reply.

Thank you.