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AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

Fig 1

Genome used by ADFR to encode the docking of a flexible ligand into a receptor with two flexible side-chains.

This figure illustrates a genome optimized by the GA implemented in ADFR for solving the problem of docking a flexible ligand with two rotatable bonds into a receptor with two flexible side-chains. The genome is the set of variables to optimize. A given set of values for these variables constitutes a docking solution also called an individual. Variables are grouped into the following genes: the ligand translation (3 values: x, y, z), rotation (4 values: quaternion), and conformation (1 torsion angle per ligand rotatable bond), and the receptor conformation (χ angles for each flexible receptor side-chain).

Fig 1

doi: https://doi.org/10.1371/journal.pcbi.1004586.g001