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Fox | AutoDock

by Stefano Forli last modified 2011-02-23 12:50

Fox is the software companion of Raccoon, and it is a prototype of a GUI for docking & virtual screening results analysis. The GUI is written in Python/TkInter and exploits the PMV 3D viewer graphical functionalities.

Fox has been designed to simplify results analysis, reports generation and structures sharing among multi-lab collaborations.

Fox has been presented and tested at Scripps Graduate Students program, the AutoDock tutorial sessions held at Scripps and at the 2010 NBCR Summer Institute.
Valuable user feedbacks have been used to improve the interface and add new functionalities.



Features

Fox automates some of the most common operations performed when analyzing virtual screening results providing the following functionalities:

  • automatic file parsing (directory/files)
  • results consistency check (i.e. target, search parameters...)
  • automatic coordinates re-clustering
  • poses filtering by energy, clustering statistics, ligand efficiency, specific residues interactions
  • results spreadsheet browser
  • 3D visualization of results and interactions
  • AutoGrid maps visualization*
  • pre-defined view styles based on target properties (trans-membrane receptors, DNA, surface binding sites...)
  • 2D view of ligand structure and schematic receptor interactions*
  • automated annotated report generation (HTML, PDF*, CSV)
  • results exporter: ligand hits PDB(QT), receptor PDB(QT), grid, parameters...
* features not available in this Alpha release.


Screenshots

Fox is organized in tabs similarly to Raccoon. The typical data flux is intended to be from left to right tabs: Input data, Filter & Analysis, Viewer, Export, although the interface is fully flexible, and required inputs can be provided in any order. If essential data is missing or inconsistencies are found, the GUI prompts it to the users.

test
Filtering tools interface


platform_linux.gif
Ligand's energy profile


platform_linux.gif
Results 3D visualization



Instructions

Fox depends on AutoDockTools v.1.5.4 or newer that must be already installed.

  • de-compress the Zip package
  • run the .py file with the PMV Python shell:
    pythonsh fox_alpha0.1.py
  • click on the "Scan directories... and select a directory containing at least one AutoDock 4.2 DLG, and follow the instructions on screen


User manual and forum support will be available when the stable version will be released

Alpha release

This is an experimental software and it is rather unstable. Therefore it should not be used for critical results analysis. Also, both input and output file formats are very likely to change in the stable version.



Please do not report bugs for the Alpha version.

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