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Abstract
Prediction of small molecule binding modes to macromolecules of known three-dimensional
structure is a problem of paramount importance in rational drug design (the "docking"
problem). We report the development and validation of the program GOLD (Genetic Optimisation
for Ligand Docking). GOLD is an automated ligand docking program that uses a genetic
algorithm to explore the full range of ligand conformational flexibility with partial
flexibility of the protein, and satisfies the fundamental requirement that the ligand
must displace loosely bound water on binding. Numerous enhancements and modifications
have been applied to the original technique resulting in a substantial increase in
the reliability and the applicability of the algorithm. The advanced algorithm has
been tested on a dataset of 100 complexes extracted from the Brookhaven Protein DataBank.
When used to dock the ligand back into the binding site, GOLD achieved a 71% success
rate in identifying the experimental binding mode.