26 S proteasome of S. pombe - Filtering out false positive crosslinks
This page is the result of a DisVis run setup within the scope of the DisVis web server tutorial.
Run Tutorial1 (Tutorial1)
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Archive of the complete run: Tutorial1.tgz
Archive of all autogenerated images: Tutorial1_images.tgz
Please cite the following papers in your work:
G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato and A.M.J.J. Bonvin.
The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes. J. Mol. Biol., Advanced Online Publication (2016).

G.C.P. van Zundert and A.M.J.J. Bonvin (2015)
DisVis: Quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes..
Bioinformatics 31, 3222-3224.
and add the following acknowledgment:
The H2020 e-Infrastructure projects West-Life (grant no. 675858), EGI-Engage-MobrainCC (grant no. 654142) and INDIGO-DataCloud (grant no. 653549) are acknowledged for the use of their web portals, which make use of the EGI infrastructure.
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Accessible Interaction Space
The accessible interaction space consistent with at least N restraints is depicted below. Use the slider to adjust N and the arrows on the side of the images to change the view.
Current Level (N): 4
Images were generated with UCSF Chimera.
Accessible Complexes
The table below lists the number of complexes consistent with at least N restraints as raw number and as fraction of all complexes.
Number of consistent restraints (N) Number of accessible complexes consistent with at least N restraints Fraction of accessible complexes consistent with at least N restraints
0 36314804 100.00 %
1 4956616 13.65 %
2 2451328 6.75 %
3 1116480 3.07 %
4 41907 0.12 %
5 195 0.00 %
6 46 0.00 %
7 0 0.00 %
z-Score
The table below features the z-Score for each restraint. The higher the score, the more likely the restraint is a false-positive. Z-scores above 1.0 are explicitly mentioned in the output of DisVis.
# Restraint Average violated fraction Standard deviation Z-score
1 A27(CA)-A18(CA) 0.59 0.36 0.01
2 A122(CA)-A125(CA) 0.65 0.25 0.23
3 A122(CA)-A128(CA) 0.81 0.10 0.84
4 A122(CA)-A127(CA) 0.56 0.37 -0.07
5 A164(CA)-A49(CA) 0.97 0.03 1.45
6 A55(CA)-A169(CA) 0.29 0.27 -1.08
7 A55(CA)-A179(CA) 0.22 0.19 -1.33
8 A54(CA)-A179(CA) 0.24 0.19 -1.29
9 A49(CA)-A188(CA) 0.92 0.13 1.23
Violations
The table below shows how often a specific restraint is violated for complexes consistent with a number of restraints. The higher the violation fraction of a specific restraint, the more likely it is to be a false-positive. Column 1 shows the number of consistent restraints N, while each following column indicates the violation fractions of a specific restraint for complexes consistent with at least N restraints. Each row thus represents the fraction of all complexes consistent with at least N restraints that violated a particular restraint.
Number of consistent restraints (N) Restraint 1 Restraint 2 Restraint 3 Restraint 4 Restraint 5 Restraint 6 Restraint 7 Restraint 8 Restraint 9
1 0.86 0.80 0.93 0.91 0.93 0.68 0.60 0.61 0.96
2 0.95 0.80 0.87 0.82 1.00 0.62 0.24 0.26 0.97
3 0.97 0.74 0.75 0.74 1.00 0.30 0.26 0.27 0.95
4 0.48 0.84 0.84 0.84 0.93 0.13 0.15 0.16 0.63
5 0.23 0.58 0.63 0.09 1.00 0.02 0.09 0.12 1.00
6 0.03 0.12 0.85 0.00 1.00 0.00 0.00 0.00 1.00