1QJP: Comparison of partiFold prediction against known X-ray crystal structure

Comparison of Secondary Structure assignment:

The Standard Output text shown below is the same output that partiFold returns, as described in the partiFold Documentation, however, the additional last (fourth) row indicates the secondary structure labeling which STRIDE infers from the protein crystal structure.

10 20 30 40 50 60 70 80 90 100 | | | | | | | | | | APKDNTWYTGAKLGWSQYHDTGLINNNGPTHENKLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGM ..TTTEEEEEEEEEEET.............TTEEEEEEEEEEEEEETTEEEEEEEEEEEEE...........EEEEEEEEEEEEEETTTTEEEEEEEEEE ..........MCMCMCMCMCMCMEEoooooooooooooooMCMCMCMCMCMCMCMiiiMCMCMCMCMCMoooooooMCMCMCMCMCMiiiMCMCMCMCMC ..........MCMCMCMCMCMCMCMoooooooooooooooEEEEMCMCMCMCMCMiiiMCMCMCMCMCMoooooooMCMCMCMCMCMiiiMCMCMCMCMC 110 120 130 140 150 160 170 | | | | | | | VWRADTYSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFG EEEEEEEETTTEEEEEEEEEEEEEEEEEEEEETTEEEEEEEEEET..............TEEEEEEEEE.. MEEEEoooooooooooMCMCMCMCMCMCMCMiiiMCMCMCMCMCMCMooooooooooMCMCMCMCMCMCM. MCMCMoooooooooooEEMCMCMCMCMCMCMiiiMCMCMCMCMCMCMooooooooooMCMCMCMCMCMCM. energy : -5.13315753962440e+01 Partition function value: 8-TMB: 1.455370e+38 Total: 1.455370e+38

Comparison of Stochastic Contact Map versus single crystal structure contacts:

Below, both axes represent the amino acid residue sequence from left-to-right and from top-to-bottom. Colored blocks indicate a beta-strand-beta-strand interaction (adjacency) between two residues within the sequence, the lower diagonal shows only those residues facing toward the center of the barrel, and the upper diagonal shows only those residues facing out of the barrel (toward the membrane).

Grayscale blocks indicate the predicted likelihood of interaction within the entire ensemble (where darker is more probable).
Red blocks are those beta-strand interactions found in the X-ray crystal structure (labeled by STRIDE).
Green blocks show the predicted minimum folding energy structure's interactions.
Blue blocks are an overlap of Red and Green blocks.


Comparison of F-measure/Sensitivity/PPV for contact map thresholds:



Comparison of Contact Probability Profile with X-ray crystal structure Debye-Waller “B-factor”:



partiFold downloadable output files:




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