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.
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|Archive of the complete run:||Example1.tgz|
|Archive of all autogenerated images:||In preparation...|
- R.V. Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin (2021). Structural biology in the clouds: The WeNMR-EOSC Ecosystem. Frontiers Mol. Biosci., 8, fmolb.2021.729513.
- G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato and A.M.J.J. Bonvin (2016)
The DisVis and PowerFit web servers: Explorative and Integrative
Modeling of Biomolecular Complexes.
J. Mol. Biol., Advanced Online Publication.
- 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.
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Accessible Interaction Space
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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|
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|
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|
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.