HADDOCK server status for docking run E2A-HPr-demo
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:
G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and A.M.J.J.Bonvin (2016). "The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes." J. Mol. Biol., 428, 720-725 (2015).
And for the use of the EGI Grid resources please please add the following acknowledgement:
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and the DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, IFCA-LCG2, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
Questions / feedback ? ask.bioexcel.eu
Summary
HADDOCK clustered 190 structures in 5 cluster(s), which represents 95.0 % 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.
Cluster 1

HADDOCK score -125.1 +/- 7.9
Cluster size 107
RMSD from the overall lowest-energy structure 1.0 +/- 0.7
Van der Waals energy -51.4 +/- 7.6
Electrostatic energy -391.2 +/- 29.3
Desolvation energy 3.4 +/- 3.9
Restraints violation energy 11.8 +/- 10.59
Buried Surface Area 1794.7 +/- 64.1
Z-Score -1.4

View the docking solutions in a Jmol structure viewer. Your browser must be Java enabled:
Nr 1 best structure Download structure
Nr 2 best structure Download structure
Nr 3 best structure Download structure
Nr 4 best structure Download structure
Cluster 2

HADDOCK score -109.0 +/- 10.3
Cluster size 55
RMSD from the overall lowest-energy structure 10.5 +/- 0.2
Van der Waals energy -49.7 +/- 2.8
Electrostatic energy -302.3 +/- 35.7
Desolvation energy 0.3 +/- 3.1
Restraints violation energy 9.5 +/- 6.23
Buried Surface Area 1790.8 +/- 56.1
Z-Score -0.8

View the docking solutions in a Jmol structure viewer. Your browser must be Java enabled:
Nr 1 best structure Download structure
Nr 2 best structure Download structure
Nr 3 best structure Download structure
Nr 4 best structure Download structure
Cluster 3

HADDOCK score -88.4 +/- 7.5
Cluster size 16
RMSD from the overall lowest-energy structure 8.4 +/- 0.9
Van der Waals energy -42.0 +/- 2.5
Electrostatic energy -228.5 +/- 24.9
Desolvation energy -2.8 +/- 3.3
Restraints violation energy 20.1 +/- 19.45
Buried Surface Area 1490.7 +/- 77.5
Z-Score 0.1

View the docking solutions in a Jmol structure viewer. Your browser must be Java enabled:
Nr 1 best structure Download structure
Nr 2 best structure Download structure
Nr 3 best structure Download structure
Nr 4 best structure Download structure
Cluster 4

HADDOCK score -74.7 +/- 7.9
Cluster size 8
RMSD from the overall lowest-energy structure 10.3 +/- 0.4
Van der Waals energy -49.5 +/- 8.3
Electrostatic energy -166.7 +/- 45.4
Desolvation energy 5.1 +/- 5.2
Restraints violation energy 29.6 +/- 18.27
Buried Surface Area 1501.8 +/- 86.9
Z-Score 0.7

View the docking solutions in a Jmol structure viewer. Your browser must be Java enabled:
Nr 1 best structure Download structure
Nr 2 best structure Download structure
Nr 3 best structure Download structure
Nr 4 best structure Download structure
Cluster 5

HADDOCK score -56.2 +/- 12.7
Cluster size 4
RMSD from the overall lowest-energy structure 8.4 +/- 0.5
Van der Waals energy -36.1 +/- 7.3
Electrostatic energy -167.8 +/- 60.3
Desolvation energy 7.1 +/- 8.6
Restraints violation energy 63.0 +/- 23.55
Buried Surface Area 1292.9 +/- 31.6
Z-Score 1.4

View the docking solutions in a Jmol structure viewer. Your browser must be Java enabled:
Nr 1 best structure Download structure
Nr 2 best structure Download structure
Nr 3 best structure Download structure
Nr 4 best 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).

interface-ligand-RMSD against HADDOCK score for water refined structures
interface-RMSD against HADDOCK score for water refined structures ligand-RMSD against HADDOCK score for water refined structures
FCC* against HADDOCK score for water refined structures Van der Waals again i-RMSD for water refined structures
Electrostatic again i-RMSD for water refined structures AIRs again i-RMSD for water refined structures
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).

Note that HADDOCK results are deleted after one week.