AutoDockFR (ADFR)

 

NOTE: this is the original (Python-based) implementation of ADFR published in PLoS

.

This version is superseeded by a much faster version relying on a C++ implementation of the Flexibility Tree and local search procedues. We strongly recommend using the new version of ADFR.

Overview

AutoDockFR (ADFR) is a new docking engine based on the AutoDock scoring function. It is designed to dock small flexible molecules into receptors, in which an unprecedented number of receptor side chains can be made flexible to simulate induced fit without prior knowledge of the side-chain undergoing conformational changes.

ADFR was shown to achieve better results than AutoDock Vina on cross-docking experiments with up to 12 flexible receptor side chains. Moreover, the runtime for docking with an increasing number of flexible receptor side chains grow exponentially with Vina while the runtime for ADFR grows linearly. These results have been submitted for publication (1).

 

Side chain conformational changes between: apo, and holo, and best energy docked solution This figure provides a comparison of the conformations of the apo (4ek3), holo complex (1ykr), and corresponding docked solution with all 12 flexible receptor side-chains displayed as ball-and-sticks. The native bound ligand is displayed as sticks with green carbon atoms and the docked solution is shown with purple carbon atoms and semi-transparent ligand surface. The apo, docked and the holo receptor side-chains are shown with orange, purple and green carbon atoms respectively. The 2 lysine side-chains in the apo conformation overlap with the space occupied by the ligand. All 12 side-chains in the docked solution underwent conformational changes, ranging from small adjustments to large changes needed to resolve steric clashes. The ligand is docked perfectly (RMSD from the crystallographic structure is 0.34 Å) and the receptor side-chains changed their conformations to accommodate the ligand binding in the correct binding mode.

 

Downloads


  • coming soon



"SEQ17"

"CDK2"

 

Documentation

The user manual along with an example can be downloaded here

 

[1] Pradeep A. Ravindranath, Stefano Forli, David S. GoodSell, Arthur J. Olson, and Michel F. Sanner. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility. PLoS Computational Biology. Submitted

This work was supported by R01 GM096888-05 grant from the National Institute of Health to Dr. M. Sanner.

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