Appendix S1. Supporting Information.

Appendix S2. Supporting Information.

Table S1 Results of the HHsearch runs versus structures in the PDB.

Figure SFQA1. “Top N" consensus CAD-score values calculated for different values of N when running the EMA-jury algorithm. Each line represents a model. Thick red lines indicate the models that were selected by the EMA-Jury algorithm.

Figure SFQA2. “Top N" consensus LDDT values calculated for different values of N when running the EMA-jury algorithm. Each line represents a model. Thick red lines indicate the models that were selected by the EMA-Jury algorithm.

Figure SFQA3. Maximum consensus scores (simple and selection-influenced) achieved for each target, using LDDT as the pairwise structural comparison method. Targets ordered by the selection-influenced values.

Figure SFQA4. Histograms of simple global consensus scores. A simple global consensus score is an average similarity of a model when compared to all the other models of the same target.

Figure SFQA5. Selection of the top model by the EMA-jury (top panel) and simple structural consensus (bottom panel) on 80 CASP13 targets. Maximum per-target LDDT scores are shown as pointing up triangles; the LDDT scores of models selected by the EMA-jury approach (top) and simple structural consensus method (bottom) are shown as pointing down triangles. The hardest to predict targets (free modeling) are in red, others in green. Vertical lines between the corresponding triangles represent the error of the selection process. Visual comparison of the top and bottom panels demonstrates that the EMA-jury method selects models closer to the best absolute value more often than the simple consensus.

Figure SFQA6. (A) Structure of the best AlphaFold CASP-COVID model aligned to the dimeric crystal structure of target C1905 (ORF3a, PDB ID 6xdc). Two copies of the monomeric model (pink and cyan) are independently aligned to different chains of the reference structure with the UCSF Chimera; (B) Structure of the best AlphaFold2 model aligned to the dimeric crystal structure of target C1908/T1064 (ORF8, PDB ID 7jtl). The figure coloring is similar to panel a. The cysteine residues involved in covalent linkage are shown as ball and sticks; (C) top: crystal structure of ORF8 (chains in black and gray) showing the crystal contact region; (C) bottom: five AlphaFold2 models (cyan) aligned to one of the chains (gray), with the crystal contact region 60–86 highlighted in orange; (D) ORF8 crystal structure colored according to the B-factor coloring scale. The crystal contact region (res. 60–86) and the high B-factor region (res. 104–110) are encircled.

Table STQA1. Disagreements between all available EMA methods when selecting top models for every target.

Table STQA2. Models selected by the EMA-jury algorithm for each target using CAD_score as the pairwise structural comparison method (models with the EMA_jury score > 0.6 are colored green, red otherwise).

Table STQA3. Models selected by EMA-jury algorithm for each target using LDDT as the pairwise structural comparison method (models with the EMA_jury score > 0.6 are colored green, red otherwise).