Welcome to the AutoDockFR Home Page

AutoDockFR – AutoDock for Flexible Receptors (ADFR), a new protein-ligand docking engine based on the AutoDock4 scoring function that efficiently handles receptor flexibility. The software has shown to handle receptor sidechain flexibility with up to 14 sidechains efficiently increasing the success rate of docking in 2 scenarios 1) considering ligand diversity where 52 CDK2 ligands were docked into 1 apo structure requiring large conformational change in the binding site (4,10 and 12 flexible receptor sidechains) 2) considering receptor diversity where 17 ligands were docked into their corresponding apo receptor requiring large conformational change (upto 14 flexible receptor sidechains). It is also demonstrated that down-weighting the receptor internal energy will increase the success of docking.

NOTE: this version of ADFR superseeds the originally published version (available here) and relies on an optimized C++ implementation of the AutoDock force field as we well as C++ implementations of the Flexibility Tree and the local search procedure, leading to a speed up of a factor of 280 compared to the originally published Python implementation for rigid docking.

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.

A tutorial is available on this web site in HTML form, or can be downloaded as a PDF file.

Copyright  Sanner Laboratory and TSRI 2016