Research Article: <scp>pso</scp>@<scp>autodock</scp>: A Fast Flexible Molecular Docking Program Based on Swarm Intelligence

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<jats:p>On the quest of novel therapeutics, molecular docking methods have proven to be valuable tools for screening large libraries of compounds determining the interactions of potential drugs with the target proteins. A widely used docking approach is the simulation of the docking process guided by a binding energy function. On the basis of the molecular docking program <jats:sc>autodock</jats:sc>, we present <jats:sc>pso</jats:sc>@<jats:sc>autodock</jats:sc> as a tool for fast flexible molecular docking. Our novel Particle Swarm Optimization (PSO) algorithms <jats:italic>var</jats:italic>CPSO and <jats:italic>var</jats:italic>CPSO‐ls are suited for rapid docking of highly flexible ligands. Thus, a ligand with 23 rotatable bonds was successfully docked within as few as 100 000 computing steps (rmsd = 0.87 Å), which corresponds to only 10% of the computing time demanded by <jats:sc>autodock</jats:sc>. In comparison to other docking techniques as <jats:sc>gold</jats:sc> 3.0, <jats:sc>dock</jats:sc> 6.0, <jats:sc>flexx</jats:sc> 2.2.0, <jats:sc>autodock</jats:sc> 3.05, and <jats:sc>sodock</jats:sc>, <jats:sc>pso</jats:sc>@<jats:sc>autodock</jats:sc> provides the smallest rmsd values for 12 in 37 protein–ligand complexes. The average rmsd value of 1.4 Å is significantly lower then those obtained with the other docking programs, which are all above 2.0 Å. Thus, <jats:sc>pso</jats:sc>@<jats:sc>autodock</jats:sc> is suggested as a highly efficient docking program in terms of speed and quality for flexible peptide–protein docking and virtual screening studies.</jats:p>

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