Output files

Click here to see some sample results.

eSimDock webserver uses AstexViewer 1 to visualize docked conformations; you can conveniently switch between different molecules. Most of the results are summarized in a big table, which includes chemical structures of your query compounds, schematic diagrams of molecular interactions generated by LIGPLOT 2 as well as several numerical scores:

  • fitness score: estimates how well a query compound fits into the binding site
  • binding score: provides general probability of binding
  • binding affinity: calculates ln(Ki) from molecular interactions

Note that fitness and binding scores are calculated using machine learning classifiers, which tend to bunch scores around 0 and 1 making them rather poor absolute estimates. However, these may still be useful for compound ranking. In addition, the table lists binding residues and provides files for download that contain individual docked conformations in SDF format.

All results can be also downloaded as a single gzipped SDF file containing all docked conformations and the corresponding numerical scores.

References

© Michal Brylinski
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