- HADDOCK server status for docking run /2931277282/3J3B_D-T_run
- Status: FINISHED
- Your HADDOCK run has successfully completed. The complete run can be downloaded as a gzipped tar file here. The file containing your docking parameters is here.
- Please cite the following paper in your work:
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin. The HADDOCK web server for data-driven biomolecular docking
Nature Protocols 5, 883-897 (2010)
doi:10.1038/nprot.2010.32- Summary
- HADDOCK clustered 20 structures in 1 cluster(s), which represents 100.0 % of the water-refined models HADDOCK generated. Note that currently the maximum number of models considered for clustering is 200.
- The statistics of the top 10 clusters are shown below. The top cluster is the most reliable according to HADDOCK. Its Z-score indicates how many standard deviations from the average this cluster is located in terms of score (the more negative the better).
- A graphical representation of the results is also provided at the bottom of the page.
- Please cite the following paper in your work:
- Cluster 1
- View the docking solutions in a Jmol structure viewer. Your browser must be Java enabled:
| HADDOCK score | -108.4 +/- 4.0 |
| Cluster size | 20 |
| RMSD from the overall lowest-energy structure | 0.4 +/- 0.2 |
| Van der Waals energy | -58.0 +/- 4.0 |
| Electrostatic energy | -147.2 +/- 2.3 |
| Desolvation energy | -21.0 +/- 5.8 |
| Restraints violation energy | 0.0 +/- 0.00 |
| Buried Surface Area | 1910.1 +/- 44.7 |
| Z-Score | 0.0 |
| Nr 1 best structure | View structure | Download structure |
| Nr 2 best structure | View structure | Download structure |
| Nr 3 best structure | View structure | Download structure |
| Nr 4 best structure | View structure | Download structure |
- Results analysis
- The results and graphics presented below are based on water-refined models generated by HADDOCK. The clusters (indicated in color in the graphs) are calculated based on the interface-ligand RMSDs calculated by HADDOCK, with the interface defined automatically based on all observed contacts. The various structural analysis (FCC, i-RMSD and l-RMSD) are made with respect to the best HADDOCK model (the one with the lowest HADDOCK score).
- Supplementary information:
- i-RMSD -> interface-RMSD calculated on the backbone (CA,C,N,O,P) atoms of all residues involved in intermolecular contact using a 10Å cutoff
l-RMSD -> ligand-RMSD calculated on the backbone atoms (CA,C,N,O,P) of all (N>1) molecules after fitting on the backbone atoms of the first (N=1) molecule
FCC -> Fraction of common contacts. The intermolecular contacts are defined based on the best HADDOCK model using a 5Å cutoff (see Rodrigues et al, Proteins 2012)
a.u. -> Arbitrary Units
The cluster averages and standard deviations are indicated by colored dots with associated error bars. The average values are calculated on the best 4 structures of each clusters (based on the HADDOCK score).