Actually, I don’t think the strategy of trying to maximize SCARB2 binding to EVA71 is optimal, because the interaction between SCARB2 and EVA71 appears to be quite flexible. When picking particles, it’s very difficult to visually identify SCARB2 density in the micrographs—it only becomes apparent after refinement and 3D classification. However, I believe many EVA71 particles likely have SCARB2 bound, just rare or not saturated.
Is there an alternative approach, such as:
- First, performing local refinement to obtain a moderate-resolution map of the SCARB2-EVA71 binding site (even if the resolution isn’t high).
- Then, using this map as a template to search for similar binding sites across all micrographs?
