Dear Dr,

 I forgot to add the comment that the protein forms dimer on the SDS-PAGE.

“Dimer Formation of a Cell-Cell Adhesion Protein, gp64 of the Cellular Slime Mold, Polysphondylium pallidum”
Plans and Cell Physiology, Vol. 36, March 1996, pages 135-139

Hiroshi

2026/07/05 14:29、落合廣 <ochiai3@icloud.com>のメール:

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