26 S proteasome of S. pombe
We applied DisVis (complete scanning) on two proteins of the 26 S proteasome of S. pombe, PRE5 (O14250) and PUP2 (Q9UT97), with 7 cross-links available (Leitner et al., 2014). The acceptable distances for the adipic acid dihydrazide (ADH) and zero-length (ZL) cross-links were set to 23 and 26 Å (Cα − Cα), respectively, as 95% of distances found in a benchmark were shorter (Leitner et al., 2014). The accessible interaction space consistent with all 7 restraints is heavily reduced to less than 0.0014% of the full interaction space. The accessible interaction space of the PUP2 chain with respect to PRE5 is furthermore overlapping with its center of mass deduced from a homology model.
Run Example2 (Example2)
Status: FINISHED
Your DisVis run has successfully completed.
Archive of the complete run: Example2.tgz
Archive of all autogenerated images: Example2_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 958264387 100.00 %
1 191843699 20.02 %
2 106552713 11.12 %
3 57655061 6.02 %
4 3193939 0.33 %
5 197591 0.02 %
6 62331 0.01 %
7 13409 0.00 %
z-Score
IMPORTANT! Complexes consistent with all restraints you provided exist indicating that there are no false positives among your restraints. The tables listing z-Scores and Violations can thus be ignored but are provided as part of the DisVis output nevertheless.
# Restraint Average violated fraction Standard deviation Z-score
1 A27(CA)-A18(CA) 0.44 0.37 0.83
2 A122(CA)-A125(CA) 0.48 0.23 1.45
3 A122(CA)-A128(CA) 0.45 0.29 1.00
4 A122(CA)-A127(CA) 0.36 0.33 -0.29
5 A55(CA)-A169(CA) 0.33 0.24 -0.80
6 A55(CA)-A179(CA) 0.30 0.23 -1.26
7 A54(CA)-A179(CA) 0.32 0.22 -0.94
Violations
IMPORTANT! Complexes consistent with all restraints you provided exist indicating that there are no false positives among your restraints. The tables listing z-Scores and Violations can thus be ignored but are provided as part of the DisVis output nevertheless.
Number of consistent restraints (N) Restraint 1 Restraint 2 Restraint 3 Restraint 4 Restraint 5 Restraint 6 Restraint 7
1 0.76 0.76 0.86 0.82 0.66 0.64 0.64
2 0.90 0.69 0.76 0.69 0.61 0.38 0.40
3 0.91 0.60 0.61 0.58 0.41 0.41 0.42
4 0.10 0.49 0.47 0.43 0.43 0.49 0.50
5 0.30 0.52 0.28 0.02 0.10 0.15 0.24
6 0.12 0.34 0.19 0.00 0.09 0.01 0.03