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![[Figure 1]](ji5028fig1mag.jpg)
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Figure 1
Overview of the DAQ-refine protocol. (1) Initial model evaluation with the DAQ score. The initially deposited model for PDB entry 7jsn chain A, which was derived from the EM map (EMDB entry EMD-22458, 3.2 Å resolution), is used as an example. The DAQ(AA) scores along the model are shown with a color scale from red [DAQ(AA) < −1.0] to blue [DAQ(AA) > 1.0]. The enlargement highlights regions (residue His230–Glu256) where DAQ(AA) is negative and thus highly likely to be incorrect. (2) MSA and template-model generation. Full MSAs are computed by MMseqs2 in ColabFold. Trimmed MSAs are generated by masking alignment data corresponding to positions in the full MSAs where the DAQ(AA) score is positive. The trimmed template model is generated by removing residue positions where the DAQ(AA) score is negative or zero from the initial model. (3) Model building by AlphaFold2. Three strategies (AF2 with full MSAs, AF2 with full MSAs + trimmed template model and AF2 with trimmed MSAs + trimmed template model) are performed. (4) Models are refined with Rosetta relax in the EM map. (5) Finally, the top-ranked model by DAQ(AA) score is selected as the final model. |
![[Figure 1]](ji5028fig1.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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