earticle

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A ligand-receptor docking program is an indispensible tool in modern pharmaceutical design. An accurate prediction of small molecular docking pose to a receptor is essential in drug design as well as molecular recognition. An effective docking program requires the ability to locate a correct binding pose in a surprisingly complex conformational space. However, there is an inherent difficulty to predict correct binding pose. The odds are more demanding than finding a needle in a haystack. This mainly comes from the flexibility of both ligand and receptor. Because the searching space to consider is so vast, receptor rigidity has been often applied in docking programs. Even nowadays the receptor may not be considered to be fully flexible although there have been some progress in search algorithm. Improving the efficiency of searching algorithm is still in great demand to explore other applications areas with inherently flexible ligand and/or receptor. In addition to classical search algorithms such as molecular dynamics, Monte Carlo, genetic algorithm and simulated annealing, rather recent algorithms such as tabu search, stochastic tunneling, particle swarm optimizations were also found to be effective. A good search algorithm would require a good balance between exploration and exploitation. It would be a good strategy to combine algorithms already developed. This composite algorithms can be more effective than an individual search algorithms.