On Jul 4, 2026, at 10:29 PM, 落合廣 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear DR.

Thank you for using chimeraX. I am very impressed with the development of protein assembly analysis technology. I am an elderly (88-year-old) biochemist.

　I have a question.

○1. Even if dimer formation is analyzed by AlphaFold 3, dimers with interfaces are not recognized at all (AlphaFold has a list of 19(?) analyzed). Why?

○2. Even though dimer formation (54 or 132 interface residues) can be seen by chimeraX, when looking at ipTM with AlphaFold, a number such as 0.19 is not recognized as a dimer. Do you think that this is because AlphaFold does not take into account that proteins such as GPI membrane proteins are kept in anti-parallel, do you have an opinion?

With best Regards

Hiroshi Ochiai

Research Institute for Electronic Sciences, Hokkaido University, 

Sapporo Japan

Emeritus Professor

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