AutoGridFR (AGFR)

Affinity maps and target files for docking

AutoGridFR (AGFR) computes the affinity maps that AutoDockFR, AutoDock CrankPep and AutoDock4 use to represent the binding site of a receptor during docking. AGFR is part of ADFRsuite.

AGFR can set the position and size of the docking box in several ways, from the command line or from a graphical user interface. It runs AutoGrid4 to calculate the affinity maps and stores them in a target file (.trg) together with metadata that describe the maps and how they were calculated. The metadata make maps easier to manage and support data provenance and reproducibility. Target files can be unzipped and the maps extracted for use with AutoDock4.

Features

  • Affinity maps for:
    • rigid receptors
    • receptors with flexible side chains
    • covalent docking
  • Water maps for hydrated docking
  • Automatic binding pocket detection with AutoSite (versions 1.0 and 1.1), which also computes translational points: promising grid locations that the ligand uses to explore the docking box during docking
  • Affinity gradients added to the maps: the map values inside the receptor are modified to create a gradient pointing toward the receptor surface. The gradient improves the performance of gradient-based search during docking, and does not change the score of poses that do not overlap the receptor.
  • Graphical user interface and command line
  • Support for data provenance and reproducibility

The AGFR graphical user interface

AGFR screenshot

AGFR screenshot

Affinity map shown as an orthoslice

Covalent ligand outlined with dashed lines

Docking box set from AutoSite fill points

Get started

Download AGFR is installed with ADFRsuite 1.0
Documentation the graphical interface, a GUI reference, FAQ
Tutorials six step-by-step tutorials with the graphical interface

License

AGFR is distributed under the Sannerlab MIT-like Source-Available License. ADFRsuite’s MSMS component, which agfrgui uses to compute surfaces, is free for non-commercial use only; see the ADFR license page.

How to cite

If you use AGFR in your work, please cite:

  • Zhang, Y.; Forli, S.; Omelchenko, A.; Sanner, M. F. AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools. J. Comput. Chem. 2019. doi:10.1002/jcc.26054

The agfr program also asks you to cite:

  • Ravindranath, P. A.; Forli, S.; Goodsell, D. S.; Olson, A. J.; Sanner, M. F. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility. PLoS Comput. Biol. 2015, 11(12), e1004586. doi:10.1371/journal.pcbi.1004586
  • Ravindranath, P. A.; Sanner, M. F. AutoSite: an automated approach for pseudo-ligands prediction, from ligand-binding sites identification to predicting key ligand atoms. Bioinformatics 2016. doi:10.1093/bioinformatics/btw367
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