The color on the surface is the electrostatic potential (-0.2 to 0.2). Note that HADDOCK results are deleted after one week. The surface is the electron density (0.01). The average values are calculated on the best 4 structures of each clusters (based on the HADDOCK score). The cluster averages and standard deviations are indicated by colored dots with associated error bars. The intermolecular contacts are defined based on the best HADDOCK model using a 5Å cutoff (see Rodrigues et al, Proteins 2012)
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) moleculeįCC -> Fraction of common contacts. 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 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). 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 results and graphics presented below are based on water-refined models generated by HADDOCK. Your browser must be Java enabled: Nr 1 best structure View the docking solutions in a Jmol structure viewer. RMSD from the overall lowest-energy structure Its Z-score indicates how many standard deviations from the average this cluster is located in terms of scoreĪ graphical representation of the results is also provided at the bottom of the page. The top cluster is the most reliable according to HADDOCK. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The statistics of the top 10 clusters are shown below. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation.
Note that currently the maximum number of models considered for clustering is 200. Summary HADDOCK clustered 193 structures in 6 cluster(s), which represents 96.5 % of the water-refined models HADDOCK generated. Questions / feedback ? Please also consider giving us some feedback by filling our online survey. " The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes." Please cite the following paper in your work: The file containing your docking parameters is here. The complete run can be downloaded as a gzipped tar file here. HADDOCK server status for docking run E2A-HPR Status: FINISHED Your HADDOCK run has successfully completed.
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