FIGURE LEGENDS
Figure 1. Prediction pipeline schematic and example targets for
manual interventions. (A) A schematic representation of the prediction
pipeline. The green blocks represent steps used in the default AF2
pipeline. Blocks with other colors represent modifications to the
pipeline. (B) An example of targets for which MSA arrangements were
performed. The y-axis represents MSA depth, and the x-axis represents
sequence position. (C) The MSA shown in B after the manual arrangement.
(D) An example of targets exhibiting a globular structure after the
refinement. (E) The refined result of the structure shown in D. MSA,
multiple sequence alignment.
Figure 2. Prediction conditions for T1173. “Semi-auto”
represents MSA results from the standard pipeline outlined in the
Materials and Methods section. “ExMSA” refers to MSA generated with an
added 196 aa at the N-terminus. “ExMSA (filtered)” denotes the ExMSA
after the MSA arrangement process detailed in the main text. (A)
MSA-depth pre- and post-manual interventions. (B) MSA depth with a focus
on y-axis values below 2000. (C) Predicted structure examples. Note that
the TM score was unavailable during the prediction season. “ColabFold”
represents the model downloaded from the ColabFold website
(https://wwwuser.gwdg.de/~mmirdit/casp15/). MSA,
multiple sequence alignment; aa, amino acid.
Figure 3. Accuracy differences between structures predicted
using MSAs generated by the PEZYFoldings pipeline (PEZY-MSA) and those
provided by the NBIS-AF2-standard and NBIS-AF2-multimer teams
(NBIS-MSA). (A) TM-scores of MODEL 1 (the model with the highest
confidence) for each single-domain target. (B) TM-scores of the best
structures for each single-domain target. (C) ΔTM-score (TM-score of
models using PEZY-MSA minus TM-score of models using NBIS-MSA) of MODEL
1 as a function of Nseq-NBIS-MSA (number of sequences in NBIS-MSA). (D)
ΔTM-score of the best models as a function of Nseq-NBIS-MSA. (E) CASP15
official Z-M1-GDT (Z-scores of MODEL 1 based on GDT-TS) for the
single-domain category submitted by PEZYFoldings as a function of
Nseq-NBIS-MSA. The results of the 52 targets used in this analysis were
plotted. The results of T1145-D1 and T1145-D2 were not plotted in E
because I did not submit MODEL 1 for this target.
Figure 4. Comparison of TM-scores for predicted structures
before and after refinement. (A) TM-scores for all submitted structures
for single-domain targets processed by the refinement model. (B) MODEL 1
structures’ TM-scores for single-domain targets. (C) Highest TM-score
among five submitted structures for single-domain targets. (D) TM-scores
for all submitted structures for multimer targets processed by the
refinement model. (E) MODEL 1 structures’ TM-scores for multimer targets
(F) Highest TM-score among five submitted structures for multimer
targets.