RNA polymerase II complex of S. cerevisiae
This example utilizes the RNA polymerase II complex of S. cerevisiae (1WCM, chain A and E) for which 6 BS3 cross-links were available (Chen et al., 2010; Kahraman et al., 2013). The allowed distance was set between 0 and 30 Å (Cβ – Cβ) for every restraint. Two false-positive restraints were added with a distance in the crystal structure of 35.7 (FP1) and 42.2 Å (FP2) to test whether they could be identified. For the setup of the run, the "Complete scanning" option was selected and a selection for the interface analysis was provided specifying 10 residues for each the fixed and the scanning chain. Applying DisVis shows that none of the 2.7 x 10^9 complexes sampled are consistent with all 8 restraints, though a small number are conforming to 7 cross-links (2037 complexes). For the latter, only restraint FP2 is violated. The accessible interaction space consistent with at least 6 restraints is less than 0.03% of the full interaction space . The density clearly indicates the position of the E-chain. Interestingly, both false-positive restraints are violated in over 99% of the complexes consistent with at least six restraints; in contrast, the highest violation percentage of a correct cross-link is only 0.1%. Thus, a high-violation percentage is an indication of a false-positive restraint.
Run Example1 (Example1)
Status: FINISHED
Your DisVis run has successfully completed.
Archive of the complete run: Example1.tgz
Archive of all autogenerated images: Example1_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 2728804709 100.00 %
1 351952997 12.90 %
2 145379581 5.33 %
3 44726037 1.64 %
4 13849208 0.51 %
5 2730966 0.10 %
6 818148 0.03 %
7 2037 0.00 %
8 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 A1003(CB)-E166(CB) 0.26 0.30 -0.79
2 A129(CB)-E161(CB) 0.30 0.29 -0.65
3 A129(CB)-E171(CB) 0.24 0.30 -0.85
4 A15(CB)-E171(CB) 0.37 0.30 -0.38
5 A934(CB)-E201(CB) 0.39 0.30 -0.29
6 A938(CB)-E201(CB) 0.36 0.31 -0.38
7 A180(CB)-E122(CB) 0.80 0.33 1.29
8 A1092(CB)-E152(CB) 1.00 0.01 2.05
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
1 0.73 0.81 0.78 0.81 0.74 0.78 0.77 0.98
2 0.68 0.62 0.59 0.72 0.50 0.50 0.97 1.00
3 0.31 0.35 0.29 0.43 0.65 0.62 0.97 1.00
4 0.08 0.15 0.06 0.24 0.65 0.60 0.96 1.00
5 0.02 0.14 0.00 0.36 0.18 0.06 0.94 1.00
6 0.00 0.00 0.00 0.00 0.00 0.00 1.00 1.00
7 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
Interaction analysis
The tables below shows how often a selected residues of the fixed and scanning chain are involved in the interaction in the complexes consistent with a specific number of restraints. The higher the interaction fraction of a specific residue is, the more likely it is involved in the complex interaction. Column 1 shows the residue ID, while each following column indicates the minimum number of restraints N. Each row thus represents the frequency that a residue of the receptor is found at the interface in complexes that are consistent with at least N restraints.
Fixed chain
5 6 7 8
161 0.000 0.000 0.000 0.000
162 0.000 0.000 0.000 0.000
163 0.000 0.000 0.000 0.000
164 0.000 0.000 0.000 0.000
165 0.000 0.000 0.000 0.000
861 0.008 0.007 0.000 0.000
862 0.007 0.011 0.003 0.000
863 0.006 0.014 0.004 0.000
864 0.001 0.003 0.001 0.000
865 0.001 0.002 0.000 0.000
Scanning chain
5 6 7 8
46 0.000 0.000 0.000 0.000
47 0.000 0.000 0.000 0.000
48 0.000 0.000 0.000 0.000
49 0.000 0.000 0.000 0.000
50 0.000 0.000 0.000 0.000
146 0.000 0.000 0.000 0.000
147 0.000 0.000 0.000 0.000
148 0.003 0.003 0.000 0.000
149 0.016 0.027 0.008 0.000
150 0.003 0.006 0.000 0.000