Predicted Contact and Distance Map Used in D-I-TASSER simulation
Contact Map
Distance Map
D-I-TASSER simulation is guided by the consensus contact map
(left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential.
In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence.
For the contact map, each dot represents a residue pair with predicted contact,
while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.
D-I-TASSER simulations generate a large ensemble of structural
conformations, i.e. decoys. These decoys are clustered by
SPICKER based on pairwise structure similarity to
report up to five final models from the five largest clusters. Models are
ranked in descending order of cluster size. If the simulations converge
well, it is possible to have less than 5 models generated, which is
usually an indication of good model quality.
(b)
The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on
significance of threading template alignments, contact map satisfaction rate,
mean absolute error between distance of model and distance of AttentionPotential, and convergence of
D-I-TASSER simulations. eTM-score is typically in the range of [0, 1],
with higher eTM-score signifies higher model confidence.
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References:
1.
Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.